IMPLEMENTATION OF FIELD RESEARCH FOR

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KARST HYPORHEIC FLOW
IN BEDROCK STREAMS AND PHREATIC CAVES
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By
Lauren B. Harrelson
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Submitted in Partial Fulfillment

of the Requirements for the

Masters of Science in Hydrology

New Mexico Institute of Mining and Technology

Department of Earth and Environmental Science

Socorro, New Mexico

April 2017







ProQuest Number: 10276371




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ABSTRACT

The number of studies focused on hyporheic exchange and related groundwater-surface

water interactions has grown exponentially in the last 20 years (Wondzell, 2015). Though
numerous studies have been published on hyporheic exchange in the sediments of rivers
and streams, bedrock streams and phreatic caves have received little attention. Key
aspects of field efforts aimed at identifying hyporheic exchange in these environments
include core recovery and analysis, and tracer experiments. This research presents new
coring technology using a submersible (to 50 meters) electric drill and a drill guide that
greatly enhances core recovery, allowing intact cores to be collected through either
vertical or horizontal drilling while wading at the surface or by submerged divers. The

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drill guide maximizes a plum hole and ensures stability of the drill during coring. We also
present an improved mechanical packer design for multilevel sampling of bedrock that
allows passive or active sampling (or tracer injection) of discrete intervals within the rock
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matrix. When installed properly the packers create effective seals with core hole walls,
isolating multiple sampling/injection intervals from one another. This helps to better
constrain specific hyporheic exchange pathways within the karst matrix. Tracers such as
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fluorescent dyes are used in conjunction with the multilevel samplers to demonstrate
hyporheic flow through the matrix, and may allow observation of active hyporheic flow
depending on the sampling scheme. Cores collected from bedrock streams and phreatic
conduits (caves) are analyzed for properties that may indicate past hyporheic flow
through the matrix, e.g. enhanced permeability development or systematic mineralogical
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variations along the length of cores. We propose a core analysis strategy that maximizes
the opportunity to observe physical and mineralogical properties that evidence hyporheic
flow origin. By utilizing mercury injection capillary pressure (MICP) analysis,
petrography, and electron microprobe analysis (EMPA) on cores collected from bedrock,
we expect to observe changes in characteristics like porosity, permeability, mineralogy,
and pore structure that may confirm the karst hyporheic hypothesis.

Keywords: karst; hyporheic; sampling; coring; stream research





ACKNOWLEDGMENTS

This work is supported by the National Science Foundation under Grant No. EAR-
1141768. I am grateful for the partnership of the Florida Geological Survey throughout
my graduate work, as well as Jerry Murphy and Barbara am Ende, who were two of our
valuable field partners that assisted in testing. I am especially appreciative of Michael
Angelo Gagliardi, who was instrumental in helping us design, develop, and test our
methods and instrumentation for this project. I also want to acknowledge Jason D. Gulley
from University of South Florida for his partnership in our research and his dedication to
see this work continue into the future.

Many thanks to Dana Ulmer-Scholle, Penelope J. Boston, and Andrew J. Luhmann for

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their service on my graduate committee, and for all of their guidance and input that
contributed to the advancement of this research. I’d like to thank Katrina Henry not only
for her collaboration on this research, including sharing her wealth of knowledge on
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scientific diving, but also for mentoring me when I first joined the Hydrology program at
New Mexico Tech. I want to pay a very special thanks to my research advisor, John L.
Wilson. I’ve come to affectionately think of John as my own personal Albus
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Dumbledore. Though he is exceedingly brilliant, he is one of the kindest, most generous
human beings I have ever met. I admire his passion for learning and teaching, and regard
him not only as an excellent advisor, but as a great friend as well. John was never too
busy to give me his time and attention, gently guiding me in my master’s work despite
his hectic schedule. John has been my teacher and advisor in more than just the academic
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realm, and for that, I owe him many thanks.

I also want to acknowledge my fellow students who uplifted, encouraged, and

collaborated with me throughout my time at New Mexico Tech. The bond of friendship
that was created in classes like, “Flow and Transport” are sure to last a lifetime. Finally I
want to thank my many friends, who constantly assured me that I was capable of
achieving my goals; my amazing parents, who believed in me, encouraged me, and
supported me with their love every step of the way; and my incredibly supportive partner,
who gave me the confidence, reassurance, and motivation I needed to finish strong.
Without the support of every person mentioned here, this work simply would not have
been possible.







TABLE OF CONTENTS
Page
LIST OF TABLES ............................................................................................................vi
LIST OF FIGURES ........................................................................................................ vii
CHAPTER 1: INTRODUCTION .................................................................................... 1
1.1 Literature Review ............................................................................................................ 1
1.2 Previous Work on Karst Hyporheic Flow..................................................................... 2
1.3 Importance of Hyporheic Research in Karst Aquifers ................................................ 2
1.4 Field Study of Karst Hyporheic Flow ............................................................................ 3
1.5 Roadmap .......................................................................................................................... 4
CHAPTER 2: DRILLING METHODS TO OBTAIN INTACT
CORES ............................................................................................................................... 5
2.1 Drill Type .......................................................................................................................... 5
2.1.1 Nemo V2 Drill Cautions and Drawbacks.................................................................... 7

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2.2 Drill Stability ................................................................................................................... 8
2.2.1 Drill Guide Improvements ........................................................................................ 12
2.3 Core Recovery ............................................................................................................... 13
2.3.1 System for Flushing Cuttings from the Drill Hole ................................................... 15
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2.3.2 Core Lifter Case ....................................................................................................... 17
2.3.3 Drilling deeper core holes ......................................................................................... 18
2.3.5 Core Transport.......................................................................................................... 19
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CHAPTER 3: MULTILEVEL SAMPLERS AND TRACER
EXPERIMENTS .............................................................................................................. 20
3.1 Packer Design for Multilevel Samplers ....................................................................... 20
3.2 Multilevel Sampler Design and Construction ............................................................. 21
3.3 Tracer Experiments ...................................................................................................... 24
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3.3.1 Use of multilevel samplers for dye trace experiments .................................................. 24

CHAPTER 4: CAVE RESTORATION ........................................................................ 29
4.1 Casting core plugs .......................................................................................................... 29
4.2 Installing core plugs ....................................................................................................... 31
CHAPTER 5: CORE ANALYSIS FOR DETECTION OF
KARST HYPORHEIC FLOW ...................................................................................... 33
5.1 Gas Permeametry and Pycnometry .............................................................................. 34
5.2 Petrography .................................................................................................................... 35
5.2.1 Image-J analysis of thin sections............................................................................... 36
5.2.2 Microscopy .................................................................................................................. 42
5.2.3 Backscatter electron imaging .................................................................................... 42
5.2.4 Factors to consider when evaluating 2D porosity ..................................................... 43
5.4 MICP analysis ................................................................................................................ 44
CHAPTER 6: SUMMARY ............................................................................................. 48
APPENDIX A. ALTERNATIVE DRILLING METHODS......................................... 50
APPENDIX B. MANUFACTURER’S INFORMATION ............................................ 54







APPENDIX C. VERTICAL DRILLING AND
COMPLICATIONS WITH STRATIGRAPHY ........................................................... 57
APPENDIX D. ALTERNATIVE DRILL STABILIZATION
METHODS ....................................................................................................................... 61
APPENDIX E. ALTERNATIVE CORE BITS ............................................................. 67
APPENDIX F. ALTERNTIVE SAMPLING TECHNOLOGY .................................. 70
APPENDIX G. ALTERNATIVE DYE TRACE DESIGN .......................................... 72
APPENDIX H. TESTS ON FGS CORES FROM MANATEE
SPRINGS STATE PARK ............................................................................................... 76
REFERENCES ................................................................................................................ 86

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LIST OF TABLES
Table Page
Table 1. 2D porosity estimates for Sewer Tunnel using Image-J to
analyze photographs of the thin sections. .......................................................................... 39
Table 2. 2D porosity estimates for Main Tunnel using Image-J to
analyze photographs of the thin sections. We made more porosity
estimates on the samples from Main Tunnel than those from Sewer
Tunnel or Blue Water Tunnel due to the high variability of the
results. ................................................................................................................................ 40
Table 3. 2D porosity estimates for Blue Water Tunnel using
Image-J to analyze photographs of the thin sections. ........................................................ 41

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Table 4. Comparison of 2D porosity estimates for near-conduit
and distal samples from Sewer Tunnel, Main Tunnel, and Blue
Water Tunnel. We did not find an apparent correlation between
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porosity and depth, or porosity and increasing distance from the
conduit. .............................................................................................................................. 41
Table 5. MICP analysis results for cores from the Santa Fe River
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and Little River Spring. ..................................................................................................... 46
Table A-1. Pneumatic drill air usage test results from New Mexico
and Florida. ........................................................................................................................ 53
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Table F-1. Foam Permeability for different pore sizes.

Permeability was calculated using equations and values given in
ASTM D3574-08. .............................................................................................................. 71
Table H-1. Imbibition time for water droplets on Manatee Springs
cores. .................................................................................................................................. 80
Table H-2. Permeability readings for cores from Manatee Springs. ................................ 83





LIST OF FIGURES
Figure Page
Figure 1. Nemo V2 Diver’s Edition underwater cordless electric
drill ...................................................................................................................................... 7
Figure 2. Triplicate foot drill guide for retrieving intact cores from
bedrock. ............................................................................................................................... 9
Figure 3. 11 ½ in of core from drill tests (8 ½ in intact) .................................................. 10
Figure 4. 28 in of cohesive core recovered using two Hoffman
Diamond core barrels threaded together............................................................................ 10
Figure 5. Core recovery as a function of drill stabilization method ................................. 11

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Figure 6. Poor core recovery associated with leverage arm drill
guide .................................................................................................................................. 12
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Figure 7. Modifications to triplicate foot drill guide ........................................................ 13
Figure 8. Hoffman Diamond Products core barrels and core bits .................................... 14
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Figure 9. Iron staining on distal end of 11 ½-in Santa Fe River
core .................................................................................................................................... 15
Figure 10. Hoffman Diamond Products water swivel for flushing
cuttings from drill hole. ..................................................................................................... 16
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Figure 11. 12V bilge pump connected to Light Monkey 30A dive
light battery for conveying water down core hole via water swivel.................................. 17
Figure 12. Core lifter case for extracting core samples from
bedrock .............................................................................................................................. 18
Figure 13. PVC core transport cases ................................................................................ 19
Figure 14. Mold for casting silicone rubber discs for 2 ¼-in
diameter multilevel samplers ............................................................................................. 21
Figure 15. Multilevel sampler components ...................................................................... 22
Figure 16. Multilevel sampler response to compression in axial
direction ............................................................................................................................. 23
Figure 17. Slim hole samplers for water sampling and tracer
injection ............................................................................................................................. 24
Figure 18. Charcoal “bugs” for detection of fluorescent dyes ......................................... 26







Figure 19. Injection of tracers via slim hole samplers ...................................................... 27
Figure 20. Injection of tracers in the conduit via tubes and pump at
the surface .......................................................................................................................... 28
Figure 21. 2-in PVC pipe molds for casting core plugs from sand,
crushed limestone, and Hydrocal FGR-95. ....................................................................... 30
Figure 22. 2-in core plugs made from sand, crushed limestone, and
Hydrocal FGR-95, shown with epoxy dispenser gun for securing
plugs in core holes ............................................................................................................. 31
Figure 23. Slabs of core from various depth intervals of conduits
at Manatee Springs ............................................................................................................ 37
Figure 24. 2D porosity estimation for thin sections using Image-J .................................. 38
Figure 25. Cores from Santa Fe River and Little River Spring are

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shown at the same scale ..................................................................................................... 45
Figure 26. Near-conduit and distal samples from Santa Fe River
and Little River Spring cores, before and after MICP analysis. ........................................ 45
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Figure 27. Porosity/permeability cross plot for samples from the
Santa Fe River and Little River Spring. ............................................................................ 46
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Figure 28. Tight porosity zone in the Santa Fe River core ............................................... 47
Figure 29. Pore throat radius plotted against pore volume in
samples from Santa Fe River core ..................................................................................... 47
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Figure A-1. Movescount data gathered by WKPP during

pneumatic drill tests ........................................................................................................... 52
Figure A-2. Pneumatic drill air usage with depth ............................................................. 52
Figure C-1. Photographs of near-conduit and distal samples from
Main Tunnel at Manatee Springs ...................................................................................... 58
Figure C-2. Photographs of near-conduit and distal samples from
Blue Water Tunnel at Manatee Springs............................................................................. 60
Figure D-1. Leverage arm drill guide ............................................................................... 63
Figure D-2. Leverage arm drill guide with V-shaped stabilization
bracket. .............................................................................................................................. 64
Figure D-3. Broken core retrieved with leverage arm drill guide
from Santa Fe River Park. We did not use any system for flushing
cuttings from the drill hole when we drilled this core. ...................................................... 66
Figure E-1. Kor-it diamond impregnated core bit ............................................................ 68







Figure E-2. Lackmond VTB Series Diamond core bit ..................................................... 69
Figure G-1. Tracer injection via modified 2 ¼-in multilevel
samplers ............................................................................................................................. 73
Figure G-2. Tracer injection via dye-saturated foam plugs.............................................. 74
Figure G-3. Dye injection via saturated foam plugs ........................................................ 74
Figure H-1. WDP test locations for cores from Manatee Springs.................................... 78
Figure H-2. Imbibition time versus distance from conduit for
WDP test on top surface of Manatee Springs cores. ......................................................... 79
Figure H-3. Imbibition time versus distance from conduit for
WDP test on 90o rotated surface of Manatee Springs cores .............................................. 79
Figure H-4. TinyPerm measurement locations for core from a)
Sewer Tunnel, b) Main Tunnel, and c) Blue Water Tunnel are

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numbered staring with #1 nearest the conduit, and extending out to
distal measurements........................................................................................................... 81
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Figure H-5. Permeability as a function of distance from conduit.
Distal measurements at 53-ft depth are excluded in this plot. ........................................... 82
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 This thesis is accepted on behalf of the faculty
of the Institute by the following committee:

John L. Wilson
______________________________________________________
Academic Advisor

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John L. Wilson
______________________________________________________
Research Advisor
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Dana S. Ulmer-Scholle
______________________________________________________
Committee Member
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Penelope J. Boston
_______________________________________________________
Committee Member
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Andrew J. Luhmann
______________________________________________________
Committee Member

I release this document to New Mexico Institute of Mining and Technology

Lauren B. Harrelson 04/28/2016

________________________________________________________
Student Signature Date
 CHAPTER 1: INTRODUCTION

Hyporheic flow, a vital process in rivers and streams, involves the mutual exchange of
river water and shallow groundwater between alluvial rivers and the porous sediment
surrounding them (Tonina and Buffington, 2009). Flow of water in the hyporheic zone is
much slower than flow in the stream, fostering sequestration and biogeochemical
processing of chemicals, especially nutrients and dissolved organic matter, and
contaminants (Vervier et al. 1992; Bourg and Bertin 1993; Hinkle et al., 2001). The range
of residence times of water in the hyporheic zone allow for a suite of different
kinetically-controlled reactions to take place that do not occur either in the stream or the
rest of the sediment surrounding it, designating the hyporheic zone as a biogeochemical
hotspot (Boulton et al., 1998; Cranswick et al., 2014). Phreatic karst conduits, underwater

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caves that carry the majority of aquifer flow below the water table, have fast flow rates
which liken them to surface streams (Field and Nash, 1997). Many aspects of karst
aquifer flow, including the exchange of water and solutes between conduits and the
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permeable rock matrix surrounding them, are still poorly understood (Field, 1993).

Wilson and Henry (2014) presented detailed mathematical models suggesting the
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presence of a hyporheic zone in karst conduits, which involves a continuous small-scale
exchange of water between the conduit and the surrounding matrix, resulting in mixed
waters from both sources. Koski and Wilson (2009) hypothesized that nutrients and
contaminants moving through a karst aquifer system undergo sequestration in the
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hyporheic zone, where they are stored temporarily, biogeochemically processed, and then
transported further downgradient. In addition to nutrient attenuation and contaminant
transport, karst hyporheic flow could play an important role in cave development.

1.1 Literature Review

The hyporheic flow phenomenon has been described by many authors across the fields of
biology, geochemistry, and hydrology, and therefore does not have one unified definition
(White, 1993). At the most basic hydrologic level, hyporheic flow implies mixing and
exchange of water between a stream and the sediment directly underneath and adjacent to
it (Sophocleous, 2002; Buffington and Tonina, 2009). In addition to water, dissolved
nutrients and contaminants are also exchanged between stream and sediment (Boano et
al., 2010; Gandy et al., 2007). Hyporheic flow occurs via downwelling and upwelling
circulation cells between the river and alluvium (Bencala, 2005), and has varying spatial
and temporal scales according to the extent of the hyporheic zone (Pinder and Sauer,
1971; Tonina and Buffington, 2009). Contaminants may be trapped in sediments and later





released due to hyporheic flow, or it may be a mechanism by which the stream is purified
due to contaminant sequestration (Fuller and Harvey, 2000).

With regard to biology, hyporheic flow has been shown to play an essential role in
sustaining a healthy stream ecosystem (Stanford and Ward, 1993). Many species, which
have been broadly termed as hyporheos (sensu Williams and Hynes, 1974), thrive in this
unique zone of mixing between shallow surface water and deep groundwater. Hyporheic
flow has influences on nutrient and contaminant transport in streams, which affects not
only the biologic life inhabiting the stream system, but also the chemical balance between
surface water and groundwater (Dahm, 1998).

1.2 Previous Work on Karst Hyporheic Flow

Previous authors have posited that hyporheic flow in karst conduits is a mechanism
which could shed light on unexplored aspects of karst aquifer flow (Koski and Wilson,

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2009; Wu and Hunkeler, 2013). Wilson and Henry (2014) pioneered this research,
identifying both a sediment hyporheic zone and a matrix hyporheic zone within karst
aquifers. They substantiated this claim by producing computational fluid dynamics
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models, which demonstrated that karst hyporheic flow is induced by small-scale pressure
variations along conduit walls that arise from wall roughness and morphology, as well as
cave sinuosity. Wu and Hunkeler (2013) used similar equations in modeling hyporheic
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flow through the sediment found in karst conduits. They posited that sediment in a karst
conduit would experience the majority of the hyporheic flow occurring, based on the
assumption that sediments have much higher permeability than the surrounding matrix
(Loop and White, 2001). They took the research a step further by simulating hyporheic
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flow through karst-conduit sediments in a laboratory analog model, showing that

hyporheic flow can be induced by bending in the conduit (i.e., conduit sinuosity) even
when the sediment surface is flat.

By utilizing simple mathematical equations and laboratory models, these authors

demonstrated that hyporheic flow is not restricted to a surface stream system. However,
this process has yet to be observed in the field. This field project seeks to observe, for the
first time, karst hyporheic flow, by observing evidence of past hyporheic flow via cores
collected from conduit walls, and active hyporheic flow via water samples collected from
cave-wall multilevel samplers during dye trace experiments.

1.3 Importance of Hyporheic Research in Karst Aquifers

As karst groundwater aquifers provide an estimated one-quarter of the world’s population
with clean drinking and municipal supply water (Ford and Williams, 2007), it is
important to understand the transportation and transformation of nutrients and







contaminants as they travel through these systems. Equally important are related
influences on downstream aquatic freshwater and near-shore marine ecosystems. The
body of knowledge on flow through young (eogenetic) karst as is found in the Upper
Floridan Aquifer (UFA) is still scarce. In contrast with telogenetic karst, which has
already experienced post-burial exposure and erosion, eogenetic karst is still undergoing
early meteoric diagenesis, and often develops a double porosity as a result (Vacher and
Mylroie, 2002; Florea and Vacher, 2006). Karst hyporheic flow could be a primary
mechanism at work in limestone units such as this, and may explain how double porosity
forms in the UFA.

In addition to supplying water for public municipal supply, the Floridan aquifer is host to
internationally recognized phreatic caves, which convey water to the state’s freshwater
springs (Florea, 2006). In recent years in the state of Florida, focus has shifted toward the
health of the state’s natural springs due to their vulnerability to contamination (Spechler

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and Halford 2001; Katz et al, 2004). Many of Florida’s once pristine springs have been
degraded due to anthropogenic activities such as agricultural development (Katz et al.,
2001), leachate from septic tanks (Veni et al., 2001), and animal waste disposal
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(Berryhill, 1989), which ultimately cause nitrate contamination (Brown et al., 2008). This
hyporheic research will help to understand how water and dissolved nutrients and
contaminants, including nitrate, are temporarily stored, processed, and released from the
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matrix at the margin of the phreatic caves. A deeper knowledge of these processes will
improve understanding of how those caves developed (speleogenesis), how they handle
natural nutrient loads and the increased load due to human development, and how they
may handle other contaminants.
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1.4 Field Study of Karst Hyporheic Flow

Although Wilson and Henry (2014) specify both matrix hyporheic flow and sediment
hyporheic flow in karst conduits, this study focuses on the former, that is, hyporheic
exchange in the permeable matrix at the margin of karst conduits. In order to try and
establish karst hyporheic flow, we suggest an approach that begins with core collection
and analysis followed by tracer experiments. Cores that are collected from conduit walls
are transported back to the lab and analyzed for spatial variability in physical,
mineralogical, and geochemical properties that may indicate the presence and nature of
hyporheic flow. Analyses attempt to indicate whether detectable differences in porosity,
permeability, pore structure, and mineralogy exist between zones along the length of a
core, its proximity to the conduit, and its likely position with respect to hyporheic flow-
paths.

We outline a number of analysis techniques aimed at detecting spatial variability of rock

properties, including gas pycnometry, petrography, mercury injection capillary pressure







(MICP) analysis, and microscopy. Our approach strategically focuses on smaller and
smaller zones of the core to comprehensively characterize porosity and permeability
along the length of the cores at various scales. Initially, non-destructive methods are used
to identify sections of the core that display changes in physical properties that may
evidence hyporheic flow influence or origin. Destructive techniques like MICP analysis
are implemented after all non-destructive avenues are exhausted. This not only ensures
the maximum amount of core is preserved throughout the analysis process, but also
reduces analysis costs, as the non-destructive techniques we outline are generally less
expensive than destructive tests. Each analysis technique illuminates a different scale and
aspect of karst matrix properties that may help decipher whether karst hyporheic flow
played a role in the intricate history of these carbonates. Water sampling and analyses
supplement core analyses to reveal any detectable differences in general chemistry of the
karst waters. Sampling equipment is utilized in tracer experiments, which illuminates
karst hyporheic flow-paths and patterns within the matrix.

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Although our primary focus is phreatic karst conduits, this work also directs
investigations of karst hyporheic flow in bedrock streams. Significant work has been
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presented on hyporheic flow in rivers with unconsolidated sediments; however, very little
attention has been given to bedrock streams. We believe that bedrock streams also
experience a continuous exchange of water between the stream and the porous karst
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matrix below it. All of the methods we present in this paper for investigation of karst
hyporheic flow in phreatic caves were developed based on tests in a bedrock stream.
Therefore, this study informs the types of investigations that can be conducted in bedrock
streams as well. This research pioneers new methods for drilling cores from bedrock
streams and phreatic caves, as well as new technology for multilevel sampling in bedrock
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formations.

1.5 Roadmap
First, in Chapter 2, I outline the methods by which cores are collected both vertically and
laterally from bedrock, including details of instrumentation design to extract intact core
samples from bedrock streams and phreatic caves. Chapter 3 details the design and
methodology for water sampling and for tracer release and detection in the conduit and
the matrix, and Chapter 4 details cave restoration at the completion of the project. In
Chapter 5, I discuss core analysis techniques, which aim to observe systematic changes in
physical, mineralogical, and geochemical properties along the length of cores and
between different cores. Finally, I summarize my findings and discuss their implications
for investigation of karst hyporheic flow in both bedrock streams and phreatic caves.



CHAPTER 2: DRILLING METHODS TO OBTAIN INTACT CORES

In order to establish karst hyporheic flow, cores must be collected from bedrock. The
cores are then transported back to the lab and analyzed for spatial variability in physical,
mineralogical, and geochemical properties that may suggest hyporheic flow influence or
origin (see Chapter 4). Properties of interest, such as porosity and permeability, are
hypothesized to vary along the length of cores due to past hyporheic flow through the
matrix, with additional variation between cores also depending on their relative position
to like hyporheic flow-paths (e.g., into or out of the matrix) (Henry and Wilson, 2010). It
is important to note that porosity and permeability are related to both depositional
environment and diagenesis in carbonate rocks. Even if we observe changes in these

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properties along the length of collected cores, it may not be an indication of karst
hyporheic flow. However, we outline a sampling method to collect cores laterally from
conduit walls, which maximizes the chance that the relatively short cores (< 5 ft long)
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may be contained within the same unit, and therefore have similar depositional and
diagenetic histories.
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Collecting intact cores is critical to analysis, as tests on continuous cores give the best
resolution of data. If cores are broken or incomplete, changes in diagenetic patterns may
be more difficult to perceive. An intact core allows continuous observation along the
entire length of core to assess patterns of change that may be attributed to past hyporheic
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flow through the matrix. Recovering intact cores from bedrock streams and phreatic
caves, however, is a challenge. We recommend specific equipment for obtaining and
preserving cores, including a special drill, drill guide, core bit, flushing system, core lifter
case, and core transportation cases.

2.1 Drill Type

In order to retrieve continuous cores, it is important that the drill power and torque are
appropriate for the application. There are a number of options for drilling underwater.
Hydraulic drills have previously been used for coral drilling operations and are
advantageous from a power perspective (Macintyre, 1996). However, because this tool
relies on a surface hydraulic compressor and hoses that supply hydraulic power to the
drill, it is not suitable for use in less accessible areas of phreatic karst conduits. A
hydraulic drill would require a considerable length of hose to reach sites in the caves
where cores would be drilled, and energy losses due to friction along the length of the
hose could significantly reduce the power it provides to the drill. A second option for







drilling underwater is a pneumatic drill fitted with an adaptor that allows it to operate
underwater off of a scuba tank (Henry et al., 2011). However, an excessive volume of air
per unit time used by the drill at depth may render it too inefficient to be a practical tool
for coring in deep caves (Appendix A).

A favorable alternative to hydraulic and pneumatic drills is a new underwater cordless

electric drill designed by Nemo Power Tools (Figure 1, Appendix B). The Nemo V2
Diver’s Edition underwater electric drill is a watertight submersible cordless drill that is
powered by an 18V 3Ah lithium-ion battery. This drill boasts twice the torque and three
times the power of standard pneumatic drills. It has reversible drilling capability, a range
of speed settings, and allows the user to adjust torque during drilling operations, as
needed. The Nemo V2 is a promising tool not only from a power perspective, but also
due to ease of use and no need to carry extra equipment (such as hoses and tanks) in the
caves. It has a maximum operating depth of 50 meters (164 ft) and is pressurized for the

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working depth with a small hand pump included with the drill.

We tested the Nemo drill in limestone of the UFA with both masonry bits and core bits.
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The testing location was at a 2-foot (ft) depth in the Santa Fe River a few miles
downstream of Ginnie Springs Outdoors in High Springs, Florida (located where Florida
Highway 47 crosses the bedrock stream south of SW County Rd 138). We used ½-inch
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(in) and 1-in masonry drill bits to test the ease with which shallow holes could be drilled
(vertically) in limestone. Holes this size would be used for installation of anchors and
small (slim hole) sampling equipment. We used a high speed and a midrange torque
setting (9-11 out of 16 on the internal scale) for drilling ½-in and 1-in diameter holes with
masonry bits. When low to moderate force was applied to the drill, the ½-in bit cut
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through the limestone easily. The ½-in holes were also used as pilot holes for 1-in bits,
which also drilled through the limestone with little resistance. All of the resultant holes
were smooth and did not crumble or collapse after they were drilled.





Figure 1. Nemo V2 Diver’s Edition underwater cordless electric drill. The dimensions of

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the drill are 17.5 x 13.3 x 6.4 in, and it weighs approximately 9 lbs.

We tested coring with the Nemo V2 drill in the same location in the Santa Fe River.
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Coring required a lower speed and the highest torque (the setting used for installing
screws) on the Nemo V2 drill. The diver operating the drill also needed to be sensitive to
adjustments of rotation direction, drilling speed, and torque settings during coring. When
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the core bit got stuck or had difficulty, the diver released the trigger, and then depressed
slightly to resume slow drilling. Then the trigger was pressed with greater force to
resume faster drilling once the core bit regained traction. When the appropriate bit and
drill guide were utilized (see later sections), cores were relatively easy to drill in the soft,
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eogenetic limestone of the UFA, and the resultant core holes had smooth walls and did
not collapse after cores were removed from the bedrock.

2.1.1 Nemo V2 Drill Cautions and Drawbacks

The Nemo V2 drill is a simple and effective tool for drilling and coring in eogenetic
limestone formations like the UFA. Drill bits with diameters measuring 1 in typically
had no trouble advancing through bedrock when we used this drill. Core bits presented
problems more often, especially when a large vug or obstacle was encountered in the
rock. This can prevent the core bit from being advanced and may render a hole unusable.
If this should happen in a cave, the core hole should be moved over a sufficient distance
and re-drilled. For attachment of equipment that requires precise placement of holes in
the rock (such as bolts for a drill guide), divers will need to be able to adapt the
placement of holes by rotating the guide as necessary. If abandoning and re-drilling in
new locations creates extra holes, the unused holes must be filled with limestone plugs to







avoid preferential flow toward the created vugs. This is especially the case near core
holes, where multilevel samplers will be installed.

Cooling of the Nemo V2 drill is vital to its performance. When the drill was submerged,
the water was effective at cooling it. When the drill was operated above water however, it
had a tendency to overheat. The manufacturer states that the drill can be used either
above or below the water, but we found that it is important to cool it by submerging in
water every few minutes (min) during operation if using above water. Battery life is
another chief concern. The drill comes with two batteries, but these cannot be changed
underwater, and it is unclear at this time how much battery life is necessary for coring
operations. If one battery fails during drilling, the divers must ascend to the surface to
change it. To avoid this, we propose having two or more drills on hand for work in
phreatic caves. When the power runs low on one drill, it can be replaced with a backup
without having to ascend.

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Drilling direction is also important for retrieving intact cores from a bedrock formation.
The switch that controls rotation direction on the Nemo V2 drill is located next to the
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trigger. Divers should be cautious not to accidentally reverse the drilling direction during
coring. When the chuck is rotating counterclockwise, the core bit is difficult to advance,
and the core contained within the barrel can get broken. Divers must ensure that the
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rotation direction is clockwise before depressing the trigger during coring operations.
Divers must also check that the collar around the drill battery is in the “locked” position
when the drill is operated underwater. When the clutch on the drill is disengaged, as it is
in the screw installation torque setting, the drill may “kick back” if obstacles are
encountered in the formation. This can cause the collar on the battery to be bumped and
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rotated to the “unlocked” position.

2.2 Drill Stability

Another vital component in recovering intact cores is drill stabilization when coring.
While coral coring has been successful with little to no drill stabilization, these are
normally vertical coring operations where gravity works in the driller’s favor (Stearn and
Colassin, 1979; Hudson et al., 1982; Adachi and Abe, 2003). In order to test for karst
hyporheic flow, we propose that cores be collected laterally from phreatic cave walls
rather than from the floor or ceiling. This maximizes the chance that the entire core will
be contained within the same stratigraphic unit (Appendix C). It also avoids working
against gravity on the cave roof, or if working with gravity on the cave floor it avoids
disturbing bottom sediment and dealing with breakdown.





Figure 2. Triplicate foot drill guide for retrieving intact cores from bedrock.

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We fabricated a small, triplicate foot drill guide to facilitate coring and enhance core
recovery (Figure 2). We used a steel fence post driver for the main body of the guide,
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cutting it to ~3-in height. We used ultra high molecular weight (UHMW) polyethylene
strips to line the inside of the guide to minimize abrasion of the core bit. The UHMW was
cut to a thickness that resulted in the ID of the drill guide being 2 ¼ in (the diameter of
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the core barrel). We welded three steel flat plates to the outside of the guide, giving it
three triangulated feet for stabilization. Each foot has a ⅜-in hole for a ½-in sleeve anchor
to be inserted in a drill hole for attaching the guide to bedrock. The triplicate foot drill
guide is small, lightweight and easy to carry, and the UHMW lining preserves the core
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barrel during coring. The height of the drill guide circular base has the strongest control
on drill stability and thus core recovery.

We recovered 8 ½ in of intact core using this drill guide when we tested coring
horizontally at a 3-ft depth underwater in the Santa Fe River 30 ft upstream of the bridge
on Highway 47 (Figure 3). In another test, we dove to a 12-ft depth in the Santa Fe River
the same distance upstream of the bridge on Highway 47. After drilling 14 in (1 core
barrel length) into the bedrock formation, we used the core lifter case to retrieve the core,
and then extracted it from the core barrel on the surface. Then, we threaded a second core
barrel onto the first and drilled another 14 in into the formation. Nearly the entire length
of recovered core (28 in total) was intact, save for 1 ½ in at one end, and a single break
between segments where the core barrels were threaded together (Figure 4). The drill
guide was not necessary for drilling the second core barrel length; the walls of the
existent 14-in core hole provided adequate drill stabilization.





Figure 3. 11 ½ in of core from drill tests (8 ½ in intact). We used the Hoffman Diamond
Products surface-set diamond core bit, triplicate foot drill guide, and Nemo V2 drill.

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Figure 4. 28 in of cohesive core recovered using two Hoffman Diamond core barrels
threaded together. a) The core was removed from bedrock in two 14-in lengths. b) The
core fit together remarkably well despite removal from bedrock in two separate pieces. c)
Core recovery was optimal. Only one 1 ½-in piece at the end of the first core extracted
was broken.

The triplicate foot drill guide yielded much better results than free drilling (not using any
drill guide at all) or using other styles of drill guides that were tested (Figure 5; Appendix
D). The guide relies on diver pushing force behind the drill, which we found was more
than sufficient for coring in the eogenetic limestone of the UFA. It is important not to put
too much pressure on the drill when coring. If the pushing force behind the drill is too
hard, the rotation of the core bit will cease and the drill will stall. Minimal pushing force
on the drill consistently resulted in ≥ 6 in of intact core when used in conjunction with a





drill guide. Attempting to force the core bit into the bedrock by pushing harder on the
drill yielded rubbly and broken cores, with individual pieces measuring no more than 3 in
long (Figure 6). Although it is possible that the cores were broken due to a compositional
control within the bedrock, coring locations were < 1 ft apart, and the rock type appeared
to be the same. This suggests that pushing force behind the drill was the likely cause of
core damage.





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Figure 5. Core recovery as a function of drill stabilization method. The length of intact
core varied greatly depending on the drill guide used. These cores were recovered using
a) no drill guide, b) the leverage arm drill guide (Appendix D), and c) the triplicate foot
drill guide.



Figure 6. Poor core recovery associated with leverage arm drill guide. Although we
recovered > 6 in of intact core in one test using the leverage arm drill guide (Appendix
D), another test in the same location in the Santa Fe River yielded non-cohesive cores due
to too much force behind the drill.

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2.2.1 Drill Guide Improvements
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We made modest further modifications to the triplicate foot drill guide. When we
installed the guide underwater, we found that we needed more flexibility for the
placement of anchors. With only ⅜-in diameter holes, all three anchor bolts had to be
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placed in almost exactly the right location and orientation to slide into the holes on the
footplates. This level of precision is difficult to achieve when diving and drilling on a
bedrock outcrop with variable morphology. The holes on the footplates were slotted and
cut to a larger diameter to create more degrees of freedom to facilitate fitting the guide
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onto the anchor bolts more easily (Figure 7). The larger holes require fender washers to
be used to secure anchors and prevent them from slipping through the wider openings.
We also found that drilling ⅜-in pilot holes prior to using the ½-in drill bit made it much
easier to start the drill holes for anchors, as well as accurately place them. One diver
should hold the triplicate foot drill guide in place while a second diver drills the ⅜-in
pilot holes at each hole in the footing plates. Then, the guide can be moved while the ½-
in holes are drilled for the anchors to be installed.





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Figure 7. Modifications to triplicate foot drill guide. Enlarging holes and cutting slots
allows more leeway in the placement and orientation of anchors in bedrock.
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2.3 Core Recovery

In addition to the drill and drill guide being suited for the application, it is also important
for the core bit to be matched to the rock type in order to retrieve intact cores (Appendix
E). Although core barrels with tungsten carbide bits have been used previously in coral
drilling in Florida (Adachi and Abe, 2003), limestone in the UFA has a different texture
than an active reef. We chose a surface-set diamond core bit (Superior Brand, AAA-
grade diamond, 70-90 stones per carat) from Hoffman Diamond Products (Appendix B),
which has one continuous grinding edge (Figure 8). Surface-set core bits are ideal for soft
rock applications, outperforming other types of bits in bedrock that is not indurated.
Using the Nemo V2 drill, we tested drilling vertically at a 2-ft depth underwater with the
surface-set core bit in the same location on the Santa Fe River. This core bit cut through
the bedrock with relative ease when we applied minimal pushing force to the drill. We
were successful at recovering a 6-in core, which was intact save for a single break caused
by prying the core free from the bedrock with hand tools.