U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2007–5137

Prepared in cooperation with the city of Rapid City and the 

West Dakota Water Development District

Analysis of Ground-Water Flow in the

Madison Aquifer using Fluorescent Dyes

Injected in Spring Creek and Rapid Creek

near Rapid City, South Dakota, 2003–04
Cover:  Photograph of mixing the Rhodamine WT dye for injection in Rapid Creek at miscellaneous gaging station 06412200

(photograph by Andrew J. Long, U.S. Geological Survey).
Analysis of Ground-Water Flow in the 

Madison Aquifer using Fluorescent Dyes 

Injected in Spring Creek and Rapid Creek 

near Rapid City, South Dakota, 2003–04

By Larry D. Putnam and Andrew J. Long

Prepared in cooperation with the city of Rapid City and the 

West Dakota Water Development District

Scientific Investigations Report 2007–5137

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2007

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Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report.

Suggested citation:

Putnam, L.D., Long, A.J., 2007, Analysis of ground-water flow in the Madison aquifer using fluorescent dyes 

injected in Spring Creek and Rapid Creek near Rapid City, South Dakota, 2003–04: U.S. Geological Survey Scientific 

Investigations Report 2007–5137, 27 p.
iii

Contents

Abstract...........................................................................................................................................................1

Introduction.....................................................................................................................................................1

Purpose and Scope ..............................................................................................................................2

Description of the Study Area ............................................................................................................2

Previous Investigations........................................................................................................................2

Acknowledgments................................................................................................................................2

Hydrogeologic Setting...................................................................................................................................2

Hydrogeology.........................................................................................................................................2

Streamflow Loss Zones........................................................................................................................6

Spring Creek .................................................................................................................................6

Rapid Creek...................................................................................................................................8

Fluorescent Dye Tracing Methods..............................................................................................................8

Dye Injections........................................................................................................................................9

Sampling Sites.....................................................................................................................................10

Sample Collection...............................................................................................................................10

Sample Analysis..................................................................................................................................12

Fluorescein..................................................................................................................................12

Rhodamine WT...........................................................................................................................12

Analysis of Ground-Water Flow Using Fluorescent Dyes.....................................................................14

Concentrations and Transit Times of Fluorescent Dyes...............................................................14

Spring Creek Loss Zone............................................................................................................14

Fluorescein Injections in 2003 ........................................................................................14

Fluorescein Injection in 2004 ..........................................................................................18

Rapid Creek Loss Zone .............................................................................................................20

Analysis of Ground-Water Flow Paths and Velocities..................................................................23

Spring Creek Area .....................................................................................................................23

Rapid Creek Area.......................................................................................................................25

Summary........................................................................................................................................................25

References Cited..........................................................................................................................................26
iv

Figures

1. Location of study area, dye injection sites, and sampling sites ...........................................3

2. Stratigraphic section for the study area...................................................................................4

3. Simplified hydrogeologic setting in the Black Hills area .......................................................5

4. Joy’s Loss swallow hole (site S4), located on south side of Spring Creek, South

Dakota.............................................................................................................................................6

5. Daily mean streamflow for station 06407500 (Spring Creek near Keystone, South

Dakota) located upstream from the streamflow loss zone....................................................7

6. Location of sampling sites, Rapid Creek, South Dakota (see figure 1, insert A)................8

7. Location of sampling sites, Rapid Creek, South Dakota (see figure 1, insert B)..............10

8. Boxplots of fluorescein concentrations in background and blank samples ....................12

9. Comparison of initial fluorescein concentrations with concentrations in the same

samples that were stored for about 1 year ............................................................................13

10. Boxplots of Rhodamine WT concentrations in background and blank samples.............13

11. Fluorescein dye breakthrough curves for well CO following three dye injections in

Spring Creek, South Dakota, in 2003........................................................................................17

12. Fluorescein dye breakthrough curves for wells NON, NAY, and CRO following three

dye injections in Spring Creek, South Dakota, in 2003 .........................................................18

13. Fluorescein dye breakthrough curve for well CO following dye injection in Spring

Creek, South Dakota, in 2004 ....................................................................................................19

14. Fluorescein dye breakthrough curves for wells NON, NAY, CRO, HH, and CSN4

following dye injection in Spring Creek, South Dakota, in 2004..........................................19

15. Rhodamine WT dye breakthrough curves for well DRU and spring TI–SP following

dye injection in Rapid Creek, South Dakota, in 2004.............................................................22

16. Rhodamine WT dye concentrations for Jackson Springs gallery samples following

injection in Rapid Creek, South Dakota, in 2004 ....................................................................22

17. Time-series data of Rhodamine WT concentrations in samples from Rapid Creek

sites and from Jackson Springs Gallery, Rapid Creek, South Dakota ...............................23

18. Comparison of fluorescein dye breakthrough curves for well NON for 2003 and 

2004 injections in Spring Creek, South Dakota ......................................................................24

Tables

1. Description of dye injections......................................................................................................9

2. Well, spring, and stream sites where samples were collected for dye analysis ............11

3. Summary of fluorometric analysis of water samples for fluorescein dye following

injections in 2003 at sites S1 (April 29), S2 (May 22), and S3 (May 29), Spring Creek,

South Dakota ...............................................................................................................................15

4. Summary of fluorometric analysis of water samples for fluorescein dye following

injection at site S4 on March 28, 2004, Spring Creek, South Dakota .................................16

5. Summary of fluorometric analysis of water samples for Rhodamine WT dye

following injection at site R1, Rapid Creek, South Dakota...................................................21

6. Estimated ground-water velocities based on dye tracing for Spring Creek, South

Dakota...........................................................................................................................................24
Conversion Factors

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

square mile (mi2) 2.590 square kilometer (km2) 

Volume

gallon (gal) 3,785 milliliter (mL) 

cubic foot (ft3) 0.02832 cubic meter (m3) 

Flow rate

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

gallon per minute (gal/min) 0.06309 liter per second (L/s)

gallon per day (gal/d) 0.003785 cubic meter per day (m3/d)

million gallons per day (Mgal/d) 0.04381 cubic meter per second (m3/s)

Mass

pound, avoirdupois (lb) 0.4536 kilogram (kg)

Vertical coordinate information is referenced to the North American Vertical Datum of 1929 

(NAVD 29).

Horizontal coordinate information is referenced to the North American Datum of 1927 (NAD 27).

Altitude, as used in this report, refers to distance above the vertical datum.

*Transmissivity: The standard unit for transmissivity is cubic foot per day per square foot times 

foot of aquifer thickness [(ft3/d)/ft2]ft. In this report, the mathematically reduced form, foot 

squared per day (ft2/d), is used for convenience.

Concentrations of chemical constituents in water are given in micrograms per liter (μg/L).

Water year (WY) is the 12–month period, October 1 through September 30, and is designated by 

the calendar year in which it ends. Thus, the water year ending September 30, 2003, is called 

“water year 2003.”
This page intentionally left blank
Analysis of Ground-Water Flow in the Madison Aquifer 

using Fluorescent Dyes Injected in Spring Creek and 

Rapid Creek near Rapid City, South Dakota, 2003–04

By Larry D. Putnam and Andrew J. Long

streamflow was about 12 ft3/s, fluorescein was detected in 

samples from six wells and time to first arrival ranged from 

0.2 to 16 days. Following injection at site S4 in 2004, the 

length of time that dye remained in the capture zone of well 

NON, which is located approximately 2 miles from the loss 

zone, was almost an order of magnitude greater than in 2003. 

For injection at site R1, Rhodamine WT was detected at well 

DRU and spring TI–SP with time to first arrival of about 

0.5 and 1.1 days and maximum concentrations of 6.2 and 

0.91 μg/L, respectively. Well DRU and spring TI–SP are 

located near the center of the Rapid Creek loss zone where the 

creek has a large meander. Measurable concentrations were 

observed for spring TI–SP as many as 109 days after the dye 

injection. The direction of a conduit flow path in the Spring 

Creek area was to the northeast with ground-water velocities 

that ranged from 770 to 6,500 feet per day. In the Rapid Creek 

loss zone, a conduit flow path east of the loss zone was not 

evident from the dye injection.

Introduction

The Madison aquifer is used extensively for water 

supplies for the city of Rapid City, S. Dak., and other suburban 

communities in the surrounding area. A better understanding 

of ground-water flow in this complex hydrologic setting is 

needed to manage and protect this important water resource. 

The Madison Limestone, which contains the Madison aquifer, 

has extensive fractures and solution-enhanced openings that 

result in large secondary porosities and permeabilities. An 

important component of recharge to the Madison aquifer is 

streamflow loss that occurs as streams cross the Madison 

Limestone outcrop. Streamflow recharge to the Madison 

aquifer is associated with conduit formation in the limestone 

and rapid ground-water velocities.

A cooperative study between the city of Rapid City, West 

Dakota Water Development District, and the U.S. Geological 

Survey (USGS) was initiated in 2003 to conduct tracer 

testing of ground-water flow in the Madison aquifer using 

environmentally safe fluorescent dyes in the Spring Creek 

and Rapid Creek areas during 2003–04. The results of 

Abstract

The Madison aquifer, which contains fractures and 

solution openings in the Madison Limestone, is used 

extensively for water supplies for the city of Rapid City and 

other suburban communities in the Rapid City, S. Dak., area. 

The 48 square-mile study area includes the west-central 

and southwest parts of Rapid City and the outcrops of the 

Madison Limestone extending from south of Spring Creek to 

north of Rapid Creek. Recharge to the Madison Limestone 

occurs when streams lose flow as they cross the outcrop. 

The maximum net loss rate for Spring and Rapid Creek loss 

zones are 21 and 10 cubic feet per second (ft3/s), respectively. 

During 2003 and 2004, fluorescent dyes were injected in the 

Spring and Rapid Creek loss zones to estimate approximate 

loca­tions of preferential flow paths in the Madison aquifer and 

to mea­sure the response and transit times at wells and springs. 

Four injections of about 2 kilograms of fluorescein dye were 

made in the Spring Creek loss zone during 2003 (sites S1, S2, 

and S3) and 2004 (site S4). Injection at site S1 was made in 

streamflow just upstream from the loss zone over a 12-hour 

period when streamflow was about equal to the maximum loss 

rate. Injections at sites S2, S3, and S4 were made in specific 

swallow holes located in the Spring Creek loss zone. Injection 

at site R1 in 2004 of 3.5 kilograms of Rhodamine WT dye was 

made in streamflow just upstream from the Rapid Creek loss 

zone over about a 28-hour period. Selected combinations of 

27 wells, 6 springs, and 3 stream sites were monitored with 

discrete samples following the injections.

For injections at sites S1–S3, when Spring Creek 

streamflow was greater than or equal to 20 ft3/s, fluorescein 

was detected in samples from five wells that were located as 

much as about 2 miles from the loss zone. Time to first arrival 

(injection at site S1) ranged from less than 1 to less than 

10 days. The maximum fluorescein concentration (injection 

at site S1) of 120 micrograms per liter (μg/L) at well CO, 

which is located adjacent to the loss zone, was similar to the 

concentration in the stream. Fluorescein arrived at well NON 

(injection at site S1), which is located about 2 miles northeast 

of the loss zone, within about 1.6 days, and the maximum 

concentration was 44 μg/L. For injection at site S4, when 
the dye tracing were used to help determine approximate 

loca­tions of preferential flow paths in the Madison aquifer 

originating from streamflow loss zones on Spring Creek and 

Rapid Creek and to mea­sure concentrations and transit times 

of a conservative tracer at wells and springs. Results of this 

study may be helpful for water managers when considering 

contamination poten­tial or the construction of new wells, and 

provide information to improve the general understanding of 

the ground-water flow in the Madison aquifer. Because of the 

numerous water supply wells in the study area and uncertainty 

in the hydraulic connections of many of these wells to rapid 

flow paths, dye injections were designed to minimize the 

possibility of concentrations large enough to discolor water in 

wells.

Purpose and Scope

The purpose of this report is to describe the results of 

tracer testing of ground-water flow in the Madison aquifer 

using fluorescent dyes in Spring Creek and Rapid Creek near 

Rapid City, S. Dak. Dye concentrations and transit times 

to downgradient sites are presented for three fluorescein 

injections in 2003 and one fluorescein injection in 2004 in the 

Spring Creek loss zone and for one Rhodamine WT injection 

in the Rapid Creek loss zone in 2004. Ground-water flow 

paths and velocities in the Rapid City area are described on the 

basis of dye tracing results.

Description of the Study Area

The 48-square-mile (mi2) study area is located on the 

east-central flank of the Black Hills (fig. 1) and includes the 

areas where Spring and Rapid Creeks cross the Madison 

Limestone outcrop. The study area includes the west-central 

and southwest parts of Rapid City and the adjacent areas 

south and west of the city. Substantial suburban development 

is occurring in the area, and numerous public and domestic 

supply wells have been constructed in the Madison aquifer. 

Land-surface altitudes range from about 4,200 feet (ft) on the 

western side of the study area to about 3,200 ft on the eastern 

side of the study area. The Madison Limestone outcrop is 

characterized by high-relief forested areas cut by deep canyons 

with entrenched meanders and steep cliffs formed in the 

limestone. The eastern part of the study area is characterized 

by less relief and fewer forested areas. Average precipitation 

during 1961 to 1990 ranged from about 19 inches (in.) on the 

western side of the study area to 18 in. on the eastern side of 

the study area (Driscoll and others, 2000).

Previous Investigations

Previous dye-tracer studies for the Madison aquifer in 

the Rapid City area include Rahn (1971), Rahn and Gries 

(1973), and Greene (1999) that examined streamflow loss to 

the Madison aquifer for Boxelder Creek, which is north of 

the study area. Anderson and others (1999) described groundwater and surface-water interactions along Rapid Creek near 

Rapid City. An overview of flow paths in the Madison aquifer 

on the basis of stable isotopes, tritium, and previous dye tests 

in the Black Hills area is provided in Naus and others (2001). 

Long and Putnam (2004) analyzed stable-isotope, time-series 

data to estimate transit times and mixing in the Madison 

aquifer in the Spring Creek area. Studies of cave development 

in the Madison Limestone in the Black Hills area include 

Howard (1964) and Ford (1989).

Acknowledgments

The authors thank the city of Rapid City for providing 

extensive assistance with the collection of water samples. 

The authors also thank the West Dakota Water Development 

District for assistance with study coordination. Also, several 

suburban public water associations and their operators were 

helpful in providing access and assistance in collecting 

samples from other supply wells. Numerous private well 

owners also provided access to their wells for the collection of 

samples. Ericka Oberembt assisted with analysis of samples 

and compilation of data. Scott Miller provided extensive 

assistance with site investigations. Andrea Putnam assisted 

with monitoring dye injections. The South Dakota Game, Fish 

and Parks (SDGFP) allowed access to springs located on the 

Cleghorn Springs Fish Hatchery grounds.

Hydrogeologic Setting

The hydrogeologic setting and the Madison aquifer for 

Rapid City and the surrounding area are described in detail 

in Long and Putnam (2002). The following summary of the 

hydrogeologic setting emphasizes the areas near Spring and 

Rapid Creeks that are relevant to dye testing.

Hydrogeology

Uplift at the end of the Cretaceous period and subsequent 

erosion created the dome-like structure and geomorphology 

of the Black Hills. Metamorphic and igneous rocks of 

Precambrian age are exposed in the central core of the Black 

Hills, whereas younger strati­graphic layers are exposed on its 

flanks. From an aerial perspective, outcrops of Paleozoic units 

form concentric rings surrounding the Precambrian core and 

dip radially outward. One of these strati­graphic layers is the 

Mississippian-age Madison Limestone, which is composed 

of karst limestone and dolostone. A stratigraphic section for 

the Rapid City area (fig. 2) and a schematic diagram of the 

hydrogeologic setting in the Black Hills area (fig. 3) describe 

the general characteristics of the rock units and their relation 

to the Madison Limestone.

   Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
T. 2 N.

T. 1 N.

T. 1 N.

T. 1 S.

R. 6 W. R. 7 W.

Creek Spring

Creek

Rapid

44

44

16

79

Sheridan

Lake

Road

CH

RR

SC

SC

RC6

RC9

DSH

DHI

DEC

CLA

DBU

RC11

CSN3

CHLN2

HR2

HH

CO

CO

CRO

NON

NAY

CSN4

06412200

06412200

06407500

06407500

435918103192200

435914103192900

RC–BB

RC–BB

S4

R1

S1

S2

S3

S1

A

B

103°20' 103°17'30" 103°15'

44°00’

44°2'30"

44°5'

Rapid

City

Base from U.S. Geological Survey digital data, 1:100,000, 1977

Rapid City Office of City Engineer map, 1:18,000, 2005

Universal Transverse Mercator projection, zone 13

0 0.5 1 2 MILES

0 0.5 1 2 KILOMETERS

Continuous-record streamflow-gaging 

 station and station number

Miscellaneous-record streamflow-gaging 

 station and station number

Stream sampling site RC-BB for Rapid 

 Creek—Label is site identification, 

 table 2

Madison Limestone outcrop

 (Strobel and others, 1999)

Dye injection site—Label is site 

 identification, table 1

Ground-water sampling site where 

 fluorescein dye was detected—Label is 

 site identification, table 2

Ground-water sampling site where dye was 

 not detected—Label is site identification, 

 table 2

Generalized flow path from Spring Creek area

 (Long and Putnam, 2002)

See figure 7

See figure 6

EXPLANATION

Black Hills

Study area

SOUTH DAKOTA

Figure 1. Location of study area, dye injection sites, and sampling sites.

Hydrogeologic Setting   
STRATIGRAPHIC UNIT DESCRIPTION THICKNESS IN FEET

ABBREVIATION

FOR

STRATIGRAPHIC

INTERVAL

SYSTEM ERATHEM

QUATERNARY

& TERTIARY (?)

UNDIFFERENTIATED SANDS AND GRAVELS 0-50 Sand, gravel, and boulders.

1,200-2,000

Light colored clays with sandstone channel fillings and local limestone lenses.Includes rhyolite, latite, trachyte, and phondite.

WHITE RIVER GROUPINTRUSIVE IGNEOUS ROCKS

TwTui TERTIARY

QTu

Principal horizon of limestone lenses forming teepee buttes.Dark-gray shale containing scattered concretions.Widely scattered limestone masses, forming small teepee buttes.Black fissile shale with concretions. 

PIERRE SHALENIOBRARA FORMATION 100-225 Impure chalk and calcareous shale.CARLILE FORMATION Turner Sand Member

Wall Creek Sands

400-750

Light-gray shale with numerous large concretions and sandy layers.Dark-gray shale.

GRANEROS GROUP

GREENHORN FORMATION

Kps

25-380

Impure slabby limestone. Weathers buff.Dark-gray calcareous shale, with thin Orman Lake limestone at base.

BELLE FOURCHE SHALE

MOWRY SHALE

MUDDY

SANDSTONE

NEWCASTLE

SANDSTONE

SKULL CREEK SHALE

300-550

Gray shale with scattered limestone concretions.Clay spur bentonite at base.

150-250

20-60

Light-gray siliceous shale. Fish scales and thin layers of bentonite.Brown to light-yellow and white sandstone.

170-270 Dark-gray to black siliceous shale.

CRETACEOUS

FALL RIVER FORMATIONLAKOTA FORMATION

INYAN KARA

GROUP

10-200 Massive to slabby sandstone.

Coarse gray to buff cross-bedded conglomeratic sandstone, interbedded with buff, red, and gray clay, especially toward top. Local fine-grained limestone. 35-700

0-2200-225

Green to maroon shale. Thin sandstone.Massive fine-grained sandstone.

250-450

0-45

Greenish-gray shale, thin limestone lenses.Glauconitic sandstone; red sandstone near middle.Red siltstone, gypsum, and limestone.

MORRISON FORMATION

UNKPAPA SS Redwater Member

Lak MemberHulett MemberStockade Beaver Mem.Canyon Spr Member

SUNDANCEFORMATIONGYPSUM SPRING FORMATION

Kik

Ju JURASSIC

Goose Egg Equivalent

SPEARFISH FORMATION T Ps R TRIASSICMINNEKAHTA LIMESTONEOPECHE SHALE Po

Pmk

250-700

125-65

Red sandy shale, soft red sandstone and siltstone with gypsum and thin limestone layers.Gypsum locally near the base.Thin to medium-bedded finely crystaline, purplish-gray laminated limestone.Red shale and sandstone. 50-135

1,2375-800

2250-550

30-60

0-60

0-100

375-400

Yellow to red cross-bedded sandstone, limestone, and anhydrite locally at top.Red shale with interbedded limestone and sandstone at base.Massive light-colored limestone. Dolomite in part. Cavernous in upper part.Pink to buff limestone. Shale locally at base.Buff dolomite and limestone.Green shale with siltstone.Massive to thin-bedded buff to purple sandstone. Greenish glauconitic shale, flaggy dolomite, and flat-pebble limestone conglomerate. Sandstone, with conglomerate locally at the base.Schist, slate, quartzite, and arkosic grit. Intruded by diorite, metamorphosed to amphibolite, and by granite and pegmatite.

PERMIAN

PENNSYLVANIAN

MISSISSIPPIAN

P Pm MINNELUSA FORMATION

MADISON (PAHASAPA) LIMESTONEENGLEWOOD FORMATION

MDme

Ou

DEVONIAN

WHITEWOOD (RED RIVER) FORMATIONWINNIPEG FORMATIONDEADWOOD FORMATIONUNDIFFERENTIATED METAMORPHICAND IGNEOUS ROCKS

OCd

pCu

ORDOVICIAN

CAMBRIAN

CENOZOIC MESOZOIC PALEOZOIC

PRECAMBRIAN

Modified from information furnished by the Department of Geology and Geological Engineering,

South Dakota School of Mines and Technology (written commun., January 1994)

0-600

- -

Interbedded sandstone, limestone, dolomite, shale, and anhydrite.

1 Modified based on drill-hole data.3 Based on Carter and others, 2001.2 Thickness based on structure contours of Minnelusa Formation, Madison Limestone, 

and Deadwood Formation tops (Carter and Redden, 1999a, 1999b, 1999c).

Figure 2. Stratigraphic section for the study area.

   Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
Precambrian metamorphic

and igneous rocks

Deadwood

Madison

Inyan Kara

Group Formation

Limestone

Limestone

Minnekahta Minnelusa

Madison

Limestone

Formation

Minnelusa

Formation

Deadwood

Formation

Alluvial

aquifer

Potentiometric

surface of

Madison

aquifer

Spring

conduit

Water

table

Cave

Flowing well

Headwater

springs

Artesian

springs

Dip of sedimentary rocks exaggerated

Relative thickness NOT TO SCALE

Major aquifers

Confining unit

EXPLANATION

South North

Figure 3. Simplified hydrogeologic setting in the Black Hills area.

The upper surface of the Madison Limestone is a 

weathered karst sur­face, unconformable with the overlying 

Pennsylvanian- and Permian-age Minnelusa Formation 

(Cattermole, 1969). The Madison aquifer is considered karstic 

because of the extensive solution enlargement of frac­tures 

resulting in major conduits that allow high-velocity groundwater flow. A localized anisotropic permeability (principal 

direction of transmissivity) has been developed by ground 

water flowing through fractures, dissolving the rock, and 

producing dissolution-enhanced conduits along the direction 

of ground-water flow (Greene and Rahn, 1995). Secondary 

permeability in the lower part of the Madison Limestone 

generally is much smaller than in the upper part (Greene, 

1993; Miller, 2005); how­ever, the lower part can have high 

permeability near outcrop areas, especially along stream 

channels. The Devonian- and Mississippian-age Englewood 

Formation, which underlies the Madison Limestone and is less 

than 60 ft thick, has similar properties to those of the lower 

Madison Limestone. The Englewood Formation is composed 

of argillaceous, dolomitic lime­stone and probably could be 

considered a member of the Madison Limestone because of its 

lithology (Gries and Martin, 1985). Strobel and others (1999) 

mapped the Madison Limestone and Englewood Formation as 

a combined unit. For simplicity, the combined unit is referred 

to in this report as the Madison Limestone outcrop (fig. 1).

The Madison Limestone was divided into four cliffforming geomorphic units by detailed geologic mapping along 

Spring Creek, Rapid Creek, and Boxelder Creek canyons 

(located just north of the study area) by Miller (2005). The 

thickness of the units described by Miller (2005) from bottom 

to top are: 130 to 165 ft (unit 1); 81 to 120 ft (unit 2); 140 to 

150 ft (unit 3); 0 to 85 ft (unit 4). Late-Mississippian erosion 

removed the upper part of unit 4 in the Boxelder and Spring 

Creek areas and all of unit 4 and part of unit 3 in the Rapid 

Creek area. Unit 1 is highly resistant to erosion with thickly 

bedded sections and forms nearly vertical cliffs. Unit 2 is 

similar; however, the bedding is thinner and cliff faces tend to 

be more irregular. Unit 3 is characterized by massive collapse 

brecciation with large angular blocks and poorly preserved 

bedding. Caves are numerous and commonly are filled with 

cemented solution breccias and cave fill. Unit 4, where 

present, is characterized by collapse brecciation with angular 

blocks. Upper cliff surfaces are rounded off because of low 

resistance to erosion and dissolution. Karst features are found 

throughout the Madison Limestone; however, they tend to be 

more common along the contacts between these geomorphic 

units (Miller, 2005).

Hydrogeologic Setting 
Figure 4. Joy’s Loss swallow hole (site S4), located on south side of Spring Creek, South Dakota.

Streamflow Loss Zones

The streamflow loss zones described in this study include 

the stream reaches of Spring and Rapid Creeks that cross 

the Madison Limestone or alluvium overlying the Madison 

Limestone. Streamflow loss occurs to identifiable swallow 

holes or to other openings in the Madison Limestone overlain 

by the alluvial deposits.

Spring Creek

The Spring Creek loss zone for the Madison Limestone 

includes about 2.3 river miles that cross the Madison 

Limestone outcrop (fig. 1). Streamflow losses or gains may 

occur within sections of the reach; however, a net loss always 

occurs over the length of the outcrop. The maximum net loss 

rate for the Madison aquifer is referred to as the loss threshold 

rate. The estimated loss threshold rate for Spring Creek is 

21 cubic feet per second (ft3/s) (Hortness and Driscoll, 1998).

Five swallow holes have been visually identified along 

the Spring Creek loss zone. Two swallow holes observed in the 

upper reaches of the loss zone are described in Miller (2005). 

The first of these swallow holes occurs at the contact between 

the Madison Limestone and the Englewood Formation, and the 

second is at the contact between units 1 and 2. The other three 

swallow holes were named by Miller (2005) and correspond to 

dye injection sites S2, S3, and S4 (fig. 1), which are described 

in the “Dye Injections” section. The names and corresponding 

dye injection site labels (fig.1) in downstream order are: Joy’s 

Loss (site S4), Deep Throat (site S2), and Lower Bend (site 

S3). These swallow holes are located at the contact between 

Madison Limestone units 2 and 3 (Miller, 2005).

 Joy’s Loss (site S4) is a Madison Limestone cave located 

on the south side of the vertical canyon wall at stream level 

(fig. 4). The ceiling of this cave ranges from about 3 to 7 ft 

above the cave floor. The cave slopes downward and away 

from the stream channel for about 50 to 100 ft, narrowing to 

small openings along the perimeter. At higher flows during 

spring, the cave is mostly flooded; at lower flows during 

summer, all water in the stream sometimes flows directly into 

the cave or into sinks underlying the alluvium, leaving nothing 

to flow in the main channel, which is at a higher altitude than 

the cave floor. Deep Throat (site S2) is just downstream from 

Joy’s Loss on the north side of the canyon wall and is similar 

 Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
0

10

20

30

40

50

60

70

10/01/02 12/31/02 04/02/03 07/02/03 10/02/03 01/01/04 04/02/04 07/02/04

DATE

DAILY MEAN DISCHARGE, IN CUBIC FEET PER SECOND 

Figure 5. Daily mean streamflow for station 06407500 (Spring Creek near Keystone, South Dakota) located upstream from the 

streamflow loss zone.

to Joy’s Loss, except the cave entrance at site S2 is smaller. 

At higher flows during spring, a steady stream branches off 

the main channel and enters a downward-sloping throat that is 

large enough for a person to crawl through for a short distance. 

While inside this cave and when water was not observed 

entering from the stream, flowing water can be heard below 

the cave floor. At lower flows during summer, some or all of 

the flow (if any) appears to bypass the cave.

On May 28, 2003, streamflow was measured 

(U.S. Geological Survey, 2004) at station 435914103192900 

just upstream from the swallow holes of sites S2 and S4 and 

at station 435918103192200 downstream from these swallow 

holes (fig. 1). Streamflow for several days prior to this paired 

measurement was relatively steady, declining from about 30 to 

25 ft3/s at station 06407500. The streamflow loss for the reach 

calculated from the measurements was 14.3 ft3/s. The stream 

reach that contains sites S2 and S4 accounts for a substantial 

part of the total streamflow loss to the Madison aquifer.

Lower Bend swallow hole (site S3) is a small depression 

(2–3 square feet) located at the edge of the stream channel. 

The vertical canyon wall composed of Madison Limestone 

rises from the edge of this depression. At higher flows during 

spring, the depression is inundated; at lower flow during 

summer, flow may branch off the main channel and sink into 

the depression rapidly. Often, streamflow disappears into the 

swallow holes upstream from site S3, and no recharge occurs 

at this swallow hole.

The median streamflow for Spring Creek for water 

years (WY) 1987–2004 for station 06407500 (fig. 1), 

which is located just upstream from the loss zone, was 

7.5 ft3/s (U.S. Geological Survey, 2005). The median annual 

streamflow was 4.0 ft3/s for WY 2003 (U.S. Geological 

Survey, 2004) and 2.1 ft3/s for WY 2004 (U.S. Geological 

Survey, 2005). Daily mean streamflow for station 06407500 

for WY 2003 and 2004 is shown in figure 5. During spring 

2003, streamflow exceeded or was near the loss threshold of 

21 ft3/s (Hortness and Driscoll, 1998) for most of April, May, 

and June. In 2004, streamflow during the spring was very low, 

and flow reached Joy’s Loss only for a brief period at the end 

of March.

Hydrogeologic Setting 
Creek

Rapid

44

Dark

Road

Nameless Cave Road

Canyon

DDA

DVA

DDA

DHU DSP

DST2

DST1

DRU

DRU

TI–SP

Rapid City

A

0 500 FEET

0 100 METERS

Base modified from U.S. Geological Survey digital data, 1:24,000, 1978 

Rapid City Office of City Engineer map 1:18,000, 2005 

Universal Transverse Mercator projection, zone 13

EXPLANATION

Ground-water sampling site where 

 Rhodamine WT was detected—

 Label is site identification, table 2

Ground-water sampling site where 

 dye was not detected—Label is 

 site identification, table 2

103°19'50" 103°19'40" 103°19'30" 103°19'20"

44°3'

44°2’50”

44°2’40”

Madison Limestone outcrop

 (Strobel and others, 1999)

Figure 6. Location of sampling sites, Rapid Creek, South Dakota (see figure 1, insert A).

Rapid Creek

The Rapid Creek loss zone for the Madison Limestone 

includes about 2.2 river miles that cross the Madison 

Limestone outcrop (fig. 1). Streamflow losses or gains may 

occur within sections of the reach; however, a net loss always 

occurs over the length of the outcrop. The maximum net loss 

rate to the Madison aquifer (referred to as the loss threshold 

rate) was estimated to be about 10 ft3/s (Hortness and Driscoll, 

1998), which could include some loss to other hydrogeologic 

units such as the Deadwood and Minnelusa aquifers. Flow 

in Rapid Creek is regulated by Pactola Dam located about 

7 miles (mi) west of the study area; therefore, streamflow 

usually exceeds the loss threshold rate.

The average altitude of the Rapid Creek loss zone is 

about 350 ft lower than the Spring Creek loss zone because 

of geologic structural features (Miller, 2005). The thickness 

of the Madison Limestone in Rapid Creek Canyon is about 

316 ft, compared to a thickness of 475 ft in Spring Creek 

Canyon. The thickness of the upper two units described 

by Miller (2005) decreases from about 225 feet in Spring 

Creek Canyon to about 90 ft in Rapid Creek Canyon. No 

easily identifiable swallow holes were noted in walking the 

streambed that crosses the Madison Limestone in the fall 

of 2004. Miller (2005) noted some depressions in the creek 

bottom that could be potential swallow holes. Discharge 

from Tittle Spring (TI–SP) (fig. 6), which is located slightly 

downstream from the center of the loss zone, generally 

ranges between 1 and 3 ft3/s (Hortness and Driscoll, 1998). 

Analysis of ground-water and surface-water interactions 

along Rapid Creek (Hines, 1991) indicated that the loss-zone 

reach consistently loses streamflow; however, intermittent 

gains also occur within sections of the loss zone. Streamflow 

measurements at sites along the loss zone (Hines, 1991) 

indicate that the streamflow loss was distributed over the 

length of the loss zone without any reach accounting for a 

majority of the loss.

Fluorescent Dye Tracing Methods

 Fluorescent dyes can be detected at very low 

concentrations in water samples by inserting glass ampoules 

containing the sample into a filter fluorometer. This instrument 

causes the dye in the sample to fluoresce when exposed to 

light of a particular band of wavelengths. The light emitted 

has a specific band of wavelengths for a particular dye. The 

fluorometer measures the relative magnitude of this emitted 

light, which is compared to known standard concentrations of 

the dye and then converted to a concentration value in units of 

mass per volume.

 Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
Two types of tracer dyes were used in this study, sodium 

fluorescein and Rhodamine WT. The two dyes emit fluorescence at different ranges of wavelengths; thus, a sample 

containing a mixture of the two dyes can be analyzed for each 

dye separately with little interference. Sodium fluorescein is 

a water soluble form of fluorescein, which also is known as 

uranine. For simplicity, the term fluorescein was used to refer 

to sodium fluorescein in the following sections. The Chemical 

Abstract Service registry numbers are 518–47–8 for sodium 

fluorescein and 37299–86–8 for Rhodamine WT.

One way of tracing ground water in karst aquifers is to 

inject a known quantity of a dye in a stream or swallow hole 

and monitor for this dye at downgradient wells and springs. 

Determining the amount of dye to inject is based on the 

understanding of the hydrologic system. Often, reconnaissance 

testing with smaller dye concentrations is needed to design 

more robust tests. The frequency of sample collection and the 

location of sampling sites also are important considerations in 

designing the dye test. Reconnaissance testing was especially 

important in this study area because of the probability of direct 

connections to numerous public-water supplies.

Table 1. Description of dye injections.

[--, none]

Dye 

injection 

site

(figure 1)

Swallow hole 

name from 

Miller (2005)

Dye

Dye quantity

(kilograms 

of active 

ingredient)

Injection period

Streamflow 

prior to 

injection

(cubic feet per 

second)

Description

S1 -- Fluorescein 2.20 8 p.m. on April 29, 

2003, to 8 a.m. on 

April 30, 2003

20 Dye was injected continuously in 

Spring Creek upstream from the 

Madison Limestone outcrop at a rate 

of about 90 micrograms per liter 

over a 12-hour period.

S2 Deep Throat Fluorescein 1.94 6 a.m. to 6:15 a.m. 

on May 22, 2003

32 Dye was injected into a small stream 

entering the swallow hole on the 

north side of Spring Creek over a 

15-minute period.

S3 Lower Bend Fluorescein 1.94 8:35 a.m. to 8:50 

a.m. on May 29, 

2003

24 Dye was injected into a small stream 

entering the swallow hole on the 

south side of Spring Creek over a 

15-minute period.

S4 Joy’s Loss Fluorescein 2.05 4 p.m. to 4:35 p.m. 

on March 28, 

2004

12 Dye was injected into the stream 

entering the swallow hole on the 

south side of Spring Creek over a 

35-minute period. 

R1 -- Rhodamine 

WT

3.52 10:00 a.m. on 

October 25, 2004, 

to 1:50 p.m. on 

October 26, 2004

21 Dye was injected continuously in 

Rapid Creek upstream from the 

Madison Limestone outcrop over 

a 27.8-hour period resulting in an 

average stream concentration of 

about 60 micrograms per liter.

Dye Injections

Four injections of fluorescein dye at sites S1–S4 were 

made during 2003–04 in the Spring Creek loss zone, and 

one injection of Rhodamine WT dye at site R1 was made 

during 2004 in the Rapid Creek loss zone (table 1; fig. 1). 

Injection at site S1 on April 29, 2003, was made in Spring 

Creek streamflow upstream from the loss zone with a 

continuous input of dye at a rate of about 90 micrograms per 

liter (μg/L) over a 12-hour period (table 1). Streamflow was 

sustained through almost the entire loss zone at this time. 

This continuous input approach was used to minimize the 

maximum dye concentration that potentially could reach 

a supply well. Also, some water supply storage reservoirs 

were filled prior to injection to minimize the potential 

concentrations that could occur in water supplies. The 

preliminary data from this injection were used to plan for 

subsequent injections in specific swallow holes. Injection 

at site S2 on May 22, 2003, was in the Deep Throat 

swallow hole, and injection at site S3 on May 29, 2003, 

was in the Lower Bend swallow hole. Injection at site S4 on 

March 28, 2004, was in the Joy’s Loss swallow hole (table 1). 

The quantity of dye that could be injected was limited due to 

the direct connection to several supply wells that was observed 

during previous injections.

Fluorescent Dye Tracing Methods 
Creek

Rapid

Canyon

Lake

Cleghorn Springs Outfall 44

Chapel

Lane

RC–AC

RC–AC

RC–BC

CWU CWU

CL–SP

FHN–SP

FHS–SP

JA–SP

JA–SP

103°18' 103°17'50” 103°17’40”

44°3'30"

44°3'25"

44°3'35"

Rapid City

Cleghorn Springs

Fish Hatchery

B

Jackson

Springs

Pumphouse

0 500 FEET

0 100 METERS

Base modified from U.S. Geological Survey digital data,

1:24,000, 1978 

Rapid City Office of City Engineer map 1:18,000, 2005 

Universal Transverse Mercator projection, zone 13

EXPLANATION

Ground-water sampling site where 

 Rhodamine WT was detected—

 Label is site identification, table 2

Ground-water sampling site where dye 

 was not detected—Label is site 

 identification, table 2

Stream sampling site for Rapid Creek—

 Label is site indentification, table 2

Figure 7. Location of sampling sites, Rapid Creek, South Dakota (see figure 1, insert B).

An injection of Rhodamine WT dye (site R1) was made 

during 2004 in the Rapid Creek loss zone (table 1; fig. 1). 

Because of numerous supply wells near the loss zone and no 

identifiable swallow holes, the injection was metered into 

Rapid Creek upstream from the loss zone at a rate of about 

60 μg/L over a 27.8-hour period (table 1). The streamflow 

during the injection was about 21 ft3/s or about double the 

loss threshold rate of 10 ft3/s (Hortness and Driscoll, 1998); 

therefore, about one-half the injected dye was assumed to 

have entered swallow holes in the Madison Limestone. A 

preliminary reconnaissance injection of fluorescein was made 

a week earlier to estimate stream transit times and design the 

injection.

Sampling Sites

Numerous supply wells completed in the Madison 

aquifer serve suburban communities and Rapid City within 

the study area. Stable iso­tope analyses by Anderson and 

others (1999), Naus and others (2001), and Long and Putnam 

(2002) indicate that Madison aquifer water south of Rapid 

City moves northward into the Rapid City area. Therefore, 

much of the water recharging the Madison aquifer from Spring 

Creek probably moves to the north or northeast toward the 

Jackson-Cleghorn Springs complex (figs. 1 and 7) converging 

with recharge from Rapid Creek and from infiltration of 

precipitation on the Madison Limestone outcrop between the 

two streams.

Sampled sites include 27 wells, 6 springs, and 3 stream 

sites (table 2; figs. 1, 6, and 7). Sampling frequency for most 

sites was daily or more frequent initially. Sampling frequency 

decreased to weekly intervals for many sites by the end of the 

sampling period. The sites that were sampled with each dye 

injection are listed in table 2.

Sample Collection

Grab samples were collected from wells and springs 

by filling an opaque 250- or 500-milliliter high-density 

polyethylene bottle with non-chlorinated water as close to the 

source as possible. Cleghorn Springs (CL–SP) (fig. 7) was 

sampled from the Cleghorn Springs Fish Hatchery collection 

gallery through a manhole. Jackson Springs (JA–SP) (fig. 7) 

was sampled from the collection gallery sump in the Jackson 

Springs pumphouse. Stream samples were collected by 

combining six random grab samples collected across the width 

of the stream.

Samples for the three stream sites (RC–BB, RC–BC, 

and RC–AC) and some of the samples for spring site JA–SP 

were collected to evaluate the interaction of Madison aquifer 

springs and Rapid Creek near Jackson Springs (fig. 6). Jackson 

(JA–SP) and Cleghorn (CL–SP) Springs (fig. 6) are two large 

springs that together discharge about 21 ft3/s from the Madison 

aquifer adjacent to Rapid Creek (Anderson and others, 1999). 

Rapid City operates an infiltration gallery in the Rapid Creek 

alluvium near Jackson Springs, which emerges in the alluvium 

and flows toward the creek. When the infiltration gallery 

is operating at full capacity, most of the spring discharge is 

captured by the gallery along with some induced infiltration 

from Rapid Creek. Cleghorn Springs emerges in the alluvium 

north and east of Jackson Springs and also flows toward Rapid 

Creek. SDGFP operates an infiltration gallery that collects 

most of Cleghorn Springs discharge for use in an adjacent fish 

hatchery. This water is circulated through the fish hatchery 

before it is returned to Rapid Creek downstream. A detailed 

description of the Jackson-Cleghorn Springs complex is 

provided in Anderson and others (1999). Measurements of dye 

concentrations in samples collected at 15-minute intervals at 

four sites, Rapid Creek above the complex (RC–BB) (fig. 1), 

10 Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
Table 2. Well, spring, and stream sites where samples were collected for dye analysis.

Sampling site 

(figures 1, 6, 

and 7)

Station 

identification 

number

U.S. Geological Survey 

local number or station name Site type Monitored tracer test(injection site, table 1)

CO 435915103185401 1S 7E 5CBDD Production well S1, S2, S3, S4

NON 440017103174301 1N 7E32ADBA Production well S1, S2, S3, S4

NAY 440007103175301 1N 7E32DABB Production well S1, S2, S3, S4

HH 440004103174001 1N 7E32DABA Production well S1, S2, S3, S4

CRO 440037103174401 1N 7E29DDC Production well S1, S2, S3, S4

CSN4 440040103181401 1N 7E29CDDB Production well S1, S2, S3, S4

SC 435930103191401 1S 7E 6ADAB Production well S1, S2, S3

CLA 440019103181801 1N 7E32BDBB Production well S1, S2, S3

RR 440126103173201 1N 7E29AAAA Irrigation well S1, S4

DEC 440142103171601 1N 7E21CBDD Domestic well S1, S2, S3, S4

CH 440223103173201 1N 7E17DDDA Production well S1, S2, S3, S4

RC11 440220103164001 1N 7E16DCDC Production well S1, S2, S3, R1

DBU 435903103181301 1S 7E 8ABAA Domestic well S2

CHLN2 440300103173501 1N 7E17AAAC2 Production well S1, S2, S3, S4, R1

HR2 435851103143501 1S 7E11ACAB Production well S1, S2, S3, S4

RC9 440342103160701 1N 7E10BCDB Production well S1, S2, S3, R1

CSN3 440059103175302 1N 7E29DBAA Production well S4

CL–SP 440327103180503 Cleghorn Springs Spring S1, S2, S3, R1

JA–SP 440327103180501 Jackson Springs Spring S1, S2, S3, R1

RC–BB 440321103181101 Rapid Creek at Braeburn Addition Stream R1

RC–AC (

1

) Rapid Creek above Cleghorn Springs 

outfall

Stream R1

RC–BC 06412900 Rapid Creek below Cleghorn Springs Stream R1

TI–SP 440243103193701 1N 7E18CBAA (Tittle Spring) Spring R1

DRU 440248103194501 1N 7E18BCDC Domestic well R1

FHS–SP 06412700 Cleghorn Springs South Channel at 

Fish Hatchery

Spring R1

FHN–SP 06412800 Cleghorn Springs North Channel at 

Fish Hatchery

Spring R1

CWU 440327103180508 1N 7E 8DBCB Spring R1

DST1 440245103192901 1N 7E18CABA Domestic well R1

DST2 440247103192101 1N 7E18BDDD1 Domestic well R1

DSP 440228103194701 1N 7E18BCAB Domestic well R1

DHU 440302103194601 1N 7E18BDBA Domestic well R1

DDA 440247103191701 1N 7E18ACCC Domestic well R1

DHI 440247103192401 1N 7E18AACB Domestic well R1

DVA 440301103192501 1N 7E18BACC Domestic well R1

DSH 440312103194201 1N 7E 7CCDD1 Domestic well R1

RC6 440526103173001 2N 7E32ADDD Production well R1

1

Station identification number not established.

Fluorescent Dye Tracing Methods 11
FLUORESCEIN CONCENTRATION, IN MICROGRAM PER LITER

Background Blank

-0.2

-0.1

0

0.1

0.2

0.3

0.4

14 48

14 Number of values 

EXPLANATION

Upper adjacent

75th percentile

Median

25th percentile

Lower adjacent

Upper outside

Figure 8. Boxplots of fluorescein concentrations in background 

and blank samples.

the Jackson Springs Gallery (JA–SP), Rapid Creek above the 

Cleghorn Springs outfall (RC–AC), and below the complex 

(RC–BC) (fig. 7) during dye injection at site R1, were made 

to provide some insight into the interactions between Rapid 

Creek, the discharge of Madison aquifer springs, and the 

alluvium along Rapid Creek.

Sample Analysis

A Turner Designs model T–700 Laboratory fluorometer 

was used for the analyses performed for this study. Jones 

(1984) and Wilson and others (1986) provide more detailed 

technical information regarding filter fluorometer operation.

Fluorescein

Fluorescein (sodium fluorescein/uranine) is a yellowgreen dye that can be detected at concentrations as low as 

0.1 μg/L (Jones, 1984). Background water samples not 

containing dye can cause fluorometer readings at higher 

concentrations than these detection limits. Some constituents 

in natural waters, such as clay and organic substances, have 

fluorescent properties, and instrument noise also may be a 

factor. Boxplots of background and blank concentrations 

(fig. 8) for water samples at selected wells indicate that 

background concentrations generally were less than 0.3 μg/L. 

Concentrations in blank samples generally were less than 

0.1 μg/L but were as much as 0.2 μg/L (fig. 8). On the 

basis of this information, the first arrival of detectable dye 

concentrations was estimated as 0.35 μg/L. Background 

concentrations at different sites can vary spatially and 

temporally. An isolated sample with this concentration may 

not indicate the presence of dye conclusively; however, an 

upward trend beginning at this concentration was assumed to 

indicate the presence of fluorescein dye.

Because fluorescein concentrations are sensitive to 

sunlight exposure, samples were collected in opaque bottles. 

To test the loss of fluorescence, samples stored for about 

1 year were reanalyzed and compared with the original 

analysis (fig. 9). The loss in dye concentration over this period 

of time averaged about 20 percent. Dye samples were usually 

collected over a several week period before analysis, and some 

loss of dye in sample storage is possible.

Rhodamine WT

Rhodamine WT is bright red at high concentrations and 

can be detected at concentrations as low as 0.01 μg/L with a 

fluorometer (Jones, 1984). The same considerations regarding 

background levels and instrument noise as described for 

fluorescein apply to Rhodamine WT, except that Rhodamine 

WT is not as sensitive to sunlight. Boxplots of Rhodamine 

WT background concentrations (fig. 10) in water samples 

collected prior to dye injection at selected wells indicate that 

background concentrations generally were less than 0.03 μg/L. 

Concentrations in blank samples generally were less than 

0.03 μg/L. Based on this information, the calculated first 

arrival of detectable dye concentrations was estimated as about 

0.06 μg/L. An isolated sample greater than this concentration 

may not indicate the presence of dye; however, an upward 

trend beginning at this concentration was assumed to indicate 

the arrival of Rhodamine WT dye.

In the analysis of samples with a filter fluorometer, 

there is a small area of overlap in the excitation wave length 

of fluorescein and Rhodamine WT around 550 nanometers 

(Jones, 1984). Samples with standard concentrations of 

fluorescein were analyzed using the Rhodamine filters in 

the filter fluorometer to quantify this potential overlap in 

wavelengths. The analysis of several different concentrations 

of fluorescein standards indicated that the presence of 

fluorescein dye did not interfere with the analysis of samples 

for Rhodamine WT.

12 Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
REPLICATE FLUORESCEIN CONCENTRATION IN SAMPLES

STORED ABOUT 1 YEAR, IN MICROGRAMS PER LITER

INITIAL FLUORESCEIN CONCENTRATION,

IN MICROGRAMS PER LITER

0

5

10

15

20

25

0 5 10 15 20 25

Figure 9. Comparison of initial fluorescein concentrations with 

concentrations in the same samples that were stored for about 

1 year.

RHODAMINE WT CONCENTRATION, IN MICROGRAM PER LITER

Background Blank

-0.03

-0.02

-0.01

0

0.01

0.02

0.03

0.05

0.04

12 62

12 Number of values 

EXPLANATION

Upper adjacent

75th percentile

Median

25th percentile

Lower adjacent

Figure 10. Boxplots of Rhodamine WT concentrations in background and blank samples.

Fluorescent Dye Tracing Methods 13
Analysis of Ground-Water Flow Using 

Fluorescent Dyes

Fluorescent dyes were used to analyze ground-water 

flow in the Madison aquifer from recharge areas in the Spring 

Creek and Rapid Creek loss zones. Dye tracing was used to 

determine dye concentrations in samples from downgradient 

sites and to estimate transit times of these conservative tracers 

to downgradient sites. Ground-water flow paths from the loss 

zones were determined based on the locations of sites where 

dye was detected. Ground-water velocities were estimated 

based on the first arrival of dye at downgradient sites.

Concentrations and Transit Times of Fluorescent 

Dyes

A summary of concentrations and transit times of 

fluorescent dyes is presented in this section of the report for 

the dye injections in the Spring Creek and Rapid Creek loss 

zones. Three injections of fluorescein dye were made in the 

Spring Creek loss zone in 2003 and one injection was made in 

2004. One injection of Rhodamine WT dye was made in the 

Rapid Creek loss zone in 2004. Breakthrough curves, which 

are plots of dye concentrations with time, are presented for 

sites where a time series of detectable dye concentrations was 

measured.

Spring Creek Loss Zone

Fluorescein dye was injected at sites S1, S2, and S3 

(fig. 1) in the Spring Creek loss zone during 2003. A total 

of 995 discrete samples (table 3) from wells and springs 

were collected and analyzed for fluorescein concentrations 

following the 2003 dye injections. In 2004, fluorescein dye 

was injected at site S4 (fig. 1) in the Spring Creek loss zone. A 

total of 158 discrete samples (table 4) from wells and springs 

were collected and analyzed for fluorescein concentrations 

following the 2004 dye injection. The fluorescein 

concentrations and transit times of the dye to downgradient 

wells and springs are summarized separately for 2003 and 

2004 injections.

Fluorescein Injections in 2003

The first injection at site S1 upstream from the Spring 

Creek loss zone was designed for reconnais­sance purposes to 

identify fast flow paths to nearby wells where poten­tial exists 

for introducing high concentrations of dye to a water supply. 

Fluorescein dye was continuously injected into Spring Creek 

with a flow of about 20 ft3/s over a 12-hour period (table 1) 

that resulted in an average in-stream fluorescein concentration 

of about 90 μg/L that entered almost all potential swallow 

holes along Spring Creek. Fluorescein dye was detected in 

samples from five wells that were located as many as 2 mi 

from the loss zone (table 3). The transit time of dye to these 

five wells was less than 10 days (table 3).

Fluorescein dye was detected at well CO (fig. 1) at 

6:30 a.m. on April 30, 2003, in the first sample collected, 

which was about 0.89 days after the injection began at site S1, 

and the concentration was 120 μg/L (table 3). At 5:15 p.m. 

that same day, another sample was collected that also had a 

fluorescein concentration of 120 μg/L. The breakthrough curve 

for well CO (fig. 11) shows that fluorescein concentrations 

increased and then decreased rapidly within a few days. When 

fluorescein dye was injected on May 22 (about 22 days after 

the first injection) into Deep Throat swallow hole (site S2), 

located on the north side of the stream about 0.5-mi upstream 

from well CO, analysis of samples collected during a 10-hour 

period following the injection did not indicate the presence 

of dye (fig. 11). When a sample was collected from well 

CO before the third injection at Lower Bend swallow hole 

(site S3) on May 29, a fluorescein concentration of 2.49 μg/L 

was measured, and the concentrations steadily decreased 

for samples collected several hours apart and for a sample 

collected the next day (fig. 11). This dye could be from 

injection at site S1 or S2, with S2 the most likely. Although 

a small set of discrete samples were collected from well CO, 

the results indicate differences in the hydraulic connection of 

well CO to individual swallow holes. Anastomosis of conduits 

near the stream channel or separate flow paths may explain the 

differences.

14 Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
Table 3. Summary of fluorometric analysis of water samples for fluorescein dye following injections in 2003 at sites S1 (April 29), S2 (May 22), and S3 (May 29), 

Spring Creek, South Dakota.[--, no data]

 Sampling site 

(figures 1, 6, 

and 7)

Station number

Beginning 

of sampling 

period

End of 

sampling 

period 

Number 

of 

samples

Fluorescein concentration

(micrograms per liter) Days to 

first 

arrival 

of dye3

Days to first peak 

dye concentration3 Maximum for all three 

injections1

Maximum 

for first 

injection 

peak

Minimum2

CO 435915103185401 04/28/2003 06/04/2003 25 120 120.00 0.30 0.89 0.89NON 440017103174301 04/30/2003 09/24/2003 56 50 43.97 .02 1.6 1.6NAY 440007103175301 04/29/2003 09/24/2003 56 15 2.19 .04 2.5 7.8

HH 440004103174001 05/01/2003 12/01/2003 75 48.6 4.83 4.08 (4) (4)

CRO 440037103174401 04/29/2003 09/24/2003 54 8.2 2.2 .10 7.8 12.7

CSN4 440040103181401 04/29/2003 07/01/2003 30 .28 -- -.04 -- --HR2 435851103143501 04/30/2003 12/01/2003 44 .25 -- .01 -- --

RR 440126103173201 04/29/2003 05/03/2003 5 5.56 -- -.11 -- --CLA 440019103181801 04/29/2003 09/24/2003 50 .23 -- -.04 -- --

ECK 440142103171601 04/28/2003 09/23/2003 33 .20 -- -.10 -- --

SC 435930103191401 04/28/2003 06/26/2003 17 5.81 5.81 -.02 -- --

CH 440223103173201 04/29/2003 12/01/2003 34 .07 -- -.30 -- --CHLN2 440300103173501 04/29/2003 12/01/2003 34 .25 -- -.02 -- --

DBU 435903103181301 05/22/2003 05/30/2003 10 5.38 -- .06 -- --

RC11 440220103164001 04/29/2003 12/01/2003 138 .24 -- -.04 -- --RC9 440342103160701 04/29/2003 10/16/2003 152 5.37 -- .00 -- --

JA–SP 440327103180501 04/29/2003 10/12/2003 159 .21 -- .00 -- --

CL–SP 440327103180503 05/05/2003 09/09/2003 23 5.37 -- -.02 -- --

1Maximum concentrations may include some overlap of previous injections with the peak concentration from a specific injection.2Negative concentrations are not possible and represent instrument noise.3Days to first arrival and peak are based on discrete samples and thus are approximate.4Concentrations were erratic because of chlorine leaching into sample through valve from the chlorination line for the well.5Isolated sample with concentration greater than 0.35 microgram per liter.

Analysis of Ground-Water Flow Using Fluorescent Dyes 15
Table 4. Summary of fluorometric analysis of water samples for fluorescein dye following injection at site S4 on March 28, 2004, Spring Creek, South Dakota.

[--, no data]

Sampling 

site

(figure 1) 

Station number

Beginning 

of sampling 

period

End of 

sampling 

period 

Number 

of 

samples

Fluorescein concentration

(micrograms per liter) Days to first 

arrival of dye2

Days to peak dye 

concentration2

Maximum Minimum1

CO 435915103185401 03/28/2004 04/13/2004 10 493 0.30 0.19 0.19NON 440017103174301 03/28/2004 06/29/2004 26 33 .00 3.7 5.0

NAY 440007103175301 03/28/2004 05/07/2004 20 26 .00 3.7 5.3

HH 440004103174001 03/29/2004 07/01/2004 16 3.8 .00 2.1 6.0CRO 440037103174401 04/01/2004 06/29/2004 21 2.0 -.06 15.9 28.7

CSN4 440040103181401 03/30/2004 05/18/2004 16 .71 .00 14.7 21.8HR2 435851103143501 04/01/2004 06/15/2004 14 .14 .04 -- --

RR 440126103173201 04/02/2004 06/29/2004 22 .16 -.05 -- --

CSN3 440059103175302 04/13/2004 06/29/2004 13 .18 .03 -- --

1Negative concentrations are not possible and represent instrument noise.2Days to first arrival and peak are based on discrete samples and thus are approximate.

16  Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
0

20

10

40

30

60

50

80

70

90

120

110

100

130

0 5 10 15 20 25 30 35 40

DAYS AFTER INJECTION AT SITE S1

FLUORESCEIN CONCENTRATION, IN MICROGRAMS PER LITER 

Injection sites and dates

Site S1 April 29, 2003

Site S2 May 22, 2003

Site S3 May 29, 2003

S1 S2 S3

S1

S2

S3

Figure 11. Fluorescein dye breakthrough curves for well CO following three dye injections in Spring Creek, South Dakota, in 2003.

The breakthrough curves for three wells (fig. 12) that 

were located 1 to 2 mi north and east of the Spring Creek loss 

zone (fig. 1) indicate a flow path to the northeast. Fluorescein 

dye also was detected at well HH in the same general area; 

however, some degradation of dye with small amounts of 

chlorine in the samples from water treatment at the well 

resulted in erratic values; therefore, the data were not shown 

on the graph of breakthrough curves. Valves were closed to 

isolate the chlorination line from the sample point; however, 

some chlorine occasionally leached through.

Fluorescein dye arrived at well NON within about 

1.6 days after the beginning of dye injection at site 

S1 (table 3). The sample from well NON had a concentration 

of 43.97 μg/L (table 3; fig. 12), which was about one-half 

the average fluorescein concentration in the stream. The first 

arrival of dye could have been earlier than 1.6 days because 

the previous sample was collected about 18 hours earlier. A 

sample from well NON collected about 2 days after injection 

directly into the Deep Throat swallow hole (site S2) had a 

concentration of about 26 μg/L (fig. 12). A sample for well 

NON collected about 1 day after injection S3 directly into the 

Lower Bend swallow hole (site S3) had a concentration of 

about 50 μg/L (table 3; fig. 12). The peak concentrations are 

approximate because of the few discrete samples collected.

Well NAY is located about 1,000 ft southwest of well 

NON (fig. 1) and is closer to the loss zone than well NON. 

Following injection at site S1, a sample collected from 

well NAY at about the same time as the sample in which 

dye was detected at NON did not indicate the presence 

of dye (fig. 12). A sample collected about 22 hours later 

had a dye concentration of 1.16 μg/L. The concentrations 

increased slightly in samples from well NAY for several 

days to a maximum concentration of 2.19 μg/L (table 3) and 

then decreased to near background levels 21 days after the 

injection (fig. 12). About 2 days after injection at site S2, the 

fluorescein concentration in a sample from well NAY was 

15 μg/L (table 3; fig. 12). Well NAY probably is near the 

preferential flow path that is connected to well NON, and the 

dye concentrations in samples from well NAY may have been 

influenced by the pumping schedule for well NAY.

The first arrival of dye at well CRO, which is located 

about 0.5 mi north of NON (fig. 1), occurred about 8 days 

after injection at site S1, with a maximum fluorescein 

concentration of about 2.2 μg/L occurring 5 days later (table 3; 

fig. 12). From this maximum, the concentration gradually 

decreased to 0.8 μg/L during the next 10 days. Injections 

at sites S2 and S3, which were made directly into swallow 

holes, resulted in fluorescein concentrations of about 7 μg/L 

for about a week beginning about 10 days after injection 

at site S2 (fig. 12). It is not known whether the maximum 

fluorescein concentration of 8.2 μg/L (table 3) at well 

CRO resulted from injection at site S2 or site S3, or from a 

combination of both injections.

Analysis of Ground-Water Flow Using Fluorescent Dyes 17
0

5

15

10

25

20

35

30

40

55

50

45

0 10 20 30 40 50 60 70 80 90 100

DAYS AFTER INJECTION AT SITE S1

FLUORESCEIN CONCENTRATION, IN MICROGRAMS PER LITER 

Injection sites and dates

Well NON (440017103174301)

Well NAY (440007103175301)

Well CRO (440037103174401)

Site S1 April 29, 2003

Site S2 May 22, 2003

Site S3 May 29, 2003

S1 S2 S3

S1

S2

S3

Figure 12. Fluorescein dye breakthrough curves for wells NON, NAY, and CRO following three dye injections in Spring Creek, South 

Dakota, in 2003.

Fluorescein Injection in 2004

The 2004 injection of fluorescein dye in Spring Creek 

was into Joy’s Loss swallow hole (site S4) when streamflow 

was about 12 ft3/s (table 1). This injection was made during 

the highest streamflow in 2004 (fig. 5), and Spring Creek 

streamflow began receding from the swallow hole soon after 

the injection. Streamflow recharge was considerably less in 

2004 than in 2003. Dye was detected at well CSN4 (fig. 1) 

in addition to the five wells where dye was detected during 

the 2003 injections (table 4). In 2004, well CSN4 was being 

utilized as a production well; whereas, in 2003 the well 

was pumped only to collect the sample. Following the 2003 

injections, the plumbing used to collect samples from well HH 

was modified to eliminate the possibility of chlorine leaching 

into the samples. Streamflow was low and transport of the 

dye was slower in 2004 compared to 2003, as shown by dye 

breakthrough curves for the six wells where dye was detected 

(figs. 13 and 14).

The maximum fluorescein concentration for well CO 

was 493 μg/L (table 4) in the first sample collected, which 

was about 0.19 day after the injection at site S4 (fig. 13). The 

fluorescein concentration decreased to about 40 μg/L the day 

after injection and to about 3 μg/L 15 days after injection 

(fig. 13). Although the connection between the swallow hole at 

site S4 and well CO was direct, with dye arrival within hours, 

substantial dye concentrations remained many days later.

Fluorescein dye arrived at well NON about 3 days after 

injection at site S4 (table 4; fig. 14). The maximum fluorescein 

concentration of 33 μg/L occurred about 5 days after injection 

(table 4). The recession in the breakthrough curve in 2004 

occurred more slowly than in 2003, with concentrations of 

about 10 μg/L remaining 25 days after injection. Fluorescein 

concentrations in samples from well NON returned to near 

background concentrations about 75 days later (fig. 14).

Fluorescein dye arrived at well NAY about 3 days 

after injection at site S4 (table 4; fig. 14). The maximum 

concentration of about 26 μg/L (fig. 14) occurred after about 

5 days (table 4) and receded to near background levels about 

40 days after injection. Dye arrived at well HH about 2 days 

after injection (table 4; fig. 14). The maximum fluorescein 

concentration of about 4 μg/L occurred about 6 days after the 

injection at site S4 (table 4; fig. 14).

Fluorescein dye arrived at well CRO about 16 days after 

injection (table 4). The maximum fluorescein concentration 

of about 2 μg/L occurred about 29 days after injection. First 

arrival of dye at well CSN4 also occurred about 15 days 

after injection at site S4, and the maximum fluorescein 

concentration of about 0.7 μg/L occurred about 22 days after 

injection (table 4; fig. 14).

18  Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
0

50

100

150

200

300

250

450

400

350

500

0 2 4 6 8 10 12 14 16 18

DAYS AFTER INJECTION AT SITE S4

FLUORESCEIN CONCENTRATION, IN MICROGRAMS PER LITER 

Injection date March 28, 2004

Figure 13. Fluorescein dye breakthrough curve for well CO following dye injection in Spring Creek, South Dakota, in 2004.

0

5

15

10

25

20

35

30

0 10 20 30 40 50 60 70 80

DAYS AFTER INJECTION AT SITE S4

FLUORESCEIN CONCENTRATION, IN MICROGRAMS PER LITER 

Injection date March 28, 2004

Well NON (440017103174301)

Well NAY (440007103175301)

Well CRO (440037103174401)

Well HH (440004103174001)

Well CSN4 (440040103181401)

Figure 14. Fluorescein dye breakthrough curves for wells NON, NAY, CRO, HH, and CSN4 following dye injection in Spring Creek, 

South Dakota, in 2004.

Analysis of Ground-Water Flow Using Fluorescent Dyes 19
Rapid Creek Loss Zone

Rhodamine WT dye was injected at site R1 (fig. 1) in the 

Rapid Creek loss zone during 2004. A total of 511 discrete 

samples (table 5) from wells, springs, and stream sites were 

collected and analyzed for Rhodamine WT concentrations 

following injection. Additional samples were collected for 

1 day at approximately 15-minute intervals from Jackson 

Spring and three stream sites to provide information on the 

interaction between Rapid Creek and Jackson Springs. A 

summary of the time-series Rhodamine WT concentrations 

in samples from the stream sites and Jackson Springs also is 

presented.

For dye tracing in the Madison aquifer, the analyses of 

samples from wells completed in and springs discharging from 

the Madison aquifer (table 5) following the injection in Rapid 

Creek loss zone indicated the presence of dye in samples from 

well DRU and spring TI–SP (fig. 15). Well DRU and spring 

TI–SP are located near the center of the loss zone where there 

is a large meander in the creek (figs. 1 and 7). The first arrival 

of dye at well DRU was about 0.5 day after injection, and the 

maximum Rhodamine WT concentration of 6.2 μg/L was at 

about 1.5 days after injection at site R1 (table 5; fig. 15). The 

first arrival of dye at spring TI–SP was about 1.1 days after 

injection, and the maximum Rhodamine WT concentration 

of 0.91 μg/L occurred about 3 days after injection (table 5; 

fig. 15). Rhodamine WT concentrations were measured in 

samples from spring TI–SP 109 days after the dye injection 

(fig. 15). The estimates of first arrival and peak transit times 

are approximate because of the few discrete samples collected.

Rhodamine WT concentrations measured in samples 

from most of the other wells and springs were less than 

0.06 μg/L (table 5) and did not indicate the presence of 

dye. The absence of detectable dye concentrations may be 

the result of the quantity of dye injected or the length of 

sampling period and does not necessarily prove that there is 

no connection to the streamflow loss zone on Rapid Creek. 

The maximum concentration of 0.45 μg/L (table 5) that 

was measured in a sample from site JA–SP collected about 

38 hours (fig. 16) after the injection began was assumed to 

represent Rhodamine WT that was induced from Rapid Creek 

by the pumping of the Jackson Springs Gallery (fig. 6) while 

streamflow containing Rhodamine WT was flowing past site 

JA–SP. Rhodamine WT concentrations for samples from 

site JA–SP (fig. 16) that were slightly greater than 0.06 μg/L 

(detectable dye concentration) occurred after the Rhodamine 

WT concentrations returned to background concentrations of 

0.035 μg/L or less for several days. The concentrations for 

7 of the 15 samples collected 15 to 30 days after injection 

from site JA–SP had concentrations that ranged from 0.07 to 

0.09 μg/L (fig. 16). Although these concentrations were 

slightly greater than the detectable dye concentration, no trend 

in concentrations was evident. The potential for movement 

of residual dye through the alluvium to the Jackson Springs 

Gallery also was a complicating factor that prevented drawing 

any conclusions from these low concentrations for samples 

collected 15 to 30 days after injection from site JA–SP.

Because of differences in the treatment requirements of 

ground water compared to ground water under the influence 

of surface water, a better understanding of the interaction 

between the Jackson Springs Gallery and Rapid Creek is an 

important issue for the city of Rapid City. The injection of 

Rhodamine WT in Rapid Creek provided an opportunity to 

compare Rhodamine WT concentrations in Rapid Creek with 

Rhodamine WT concentrations in the Jackson Springs Gallery 

with various pumping rates from the gallery.

For a 16-hour period on the day following the beginning 

of the 2004 Rapid Creek injection, samples from Jackson 

Springs Gallery (site JA–SP) and three stream sites (RC–BB, 

RC–AC, RC–BC) surrounding the Jackson-Cleghorn Springs 

complex (figs. 1 and 7) were collected (fig. 17). Site RC–BB 

is upstream from the Jackson-Cleghorn Springs complex, 

and site RC–AC is located just upstream from the Cleghorn 

Springs Fish Hatchery outfall. Site RC–BC is located 

downstream from the Cleghorn Springs Fish Hatchery outfall. 

Pumping from the Jackson Springs Gallery was 1,800 gallons 

per minute (gal/min) prior to the injection of dye until 10 a.m. 

The pumping rate was increased to 3,100 gal/min from 10 a.m. 

to 1 p.m., then to 4,500 gal/min for the remainder of the day 

(fig. 17).

The average Rhodamine WT concentrations for the three 

stream sites were 32.12 μg/L for site RC–BB, 24.36 μg/L for 

site RC–AC, and 13.47 μg/L for site RC–BC (fig. 17). The 

Rhodamine WT concentrations for Jackson Springs Gallery 

increased gradually as the pumping rate of the gallery was 

increased. The changes in Rhodamine WT concentrations 

were not abrupt in the Jackson Springs Gallery (site JA–SP) 

when the pumping rates were increased. More than 10 hours 

after the pumping rate was increased to 4,500 gal/min, the 

dye concentration gradually increased from 0.16 μg/L to 

0.45 μg/L in samples from site JA–SP (fig. 17). The average 

concentration in the stream over this period was about 

25 to 30 μg/L. At the end of the 10-hour period at the high 

pumping rate, the Rhodamine WT concentration in samples 

from site JA–SP was less than 2 percent of the Rhodamine 

WT concentration in the stream. The Rhodamine WT 

concentrations were still increasing at the end of the sampling 

period.

20 Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
Table 5. Summary of fluorometric analysis of water samples for Rhodamine WT dye following injection at site R1, Rapid Creek, South Dakota.

[--, no data]

Sampling site

(figures 1 and 7) Station number

Beginning 

of sampling 

period

End of 

sampling 

period

Number of 

samples

Rhodamine WT concentration

(micrograms per liter) Days to first arrival of dye2 Days to peak dye concentration2 Maximum Minimum1

TI–SP 440243103193701 10/22/2004 02/11/2005 14 0.91 0.013 1.13 3.34DRU 440248103194501 10/24/2004 11/01/2004 13 6.2 .020 .51 1.5CWU 440327103180508 10/08/2004 04/26/2005 17 .043 .000 -- --DDA 440247103191701 10/20/2004 02/24/2005 17 .032 .006 -- --DHU 440302103194601 10/19/2004 03/30/2005 21 .029 -.006 -- --FHN–SP 06412800 10/26/2004 04/26/2005 13 .027 .000 -- --FHS–SP 06412700 10/26/2004 04/26/2005 13 .027 .000 -- --DST2 440247103192101 10/26/2004 03/30/2005 20 .029 -.006 -- --DST1 440245103192901 10/26/2004 03/30/2005 18 .037 -.004 -- --DSP 440228103194701 10/28/2004 12/24/2004 11 .023 -.013 -- --DSH 440312103194201 10/19/2004 03/30/2005 21 .020 -.008 -- --DVA 440301103192501 11/05/2004 03/30/2005 15 .023 -.004 -- --CHLN2 440300103173501 10/28/2004 02/24/2005 9 .024 .000 -- --DHI 440247103192401 10/28/2004 03/30/2005 21 .050 .000 -- --

JA–SP 440327103180501 10/22/2004 04/26/2005 190 3.45 .016 -- --

CL–SP 440327103180503 10/19/2004 04/26/2005 23 .047 .003 -- --

RC9 440342103160701 10/27/2004 04/27/2005 55 4.063 -.025 -- --

RC6 440526103173001 10/07/2004 12/01/2004 20 .037 -.021 -- --

1Negative concentrations are not possible and represent instrument noise.2Days to first arrival and peak are based on discrete samples and thus are approximate.3Maximum Rhodamine WT concentration is from induced flow from Rapid Creek and does not represent ground-water flow through the Madison aquifer.4Isolated sample with concentration greater than 0.06 microgram per liter.

Analysis of Ground-Water Flow Using Fluorescent Dyes 21
0

1

2

3

4

6

5

7

0 10 20 30 40 50 60 70 80 90 100 110

DAYS AFTER INJECTION AT SITE R1

RHODAMINE WT CONCENTRATION, IN MICROGRAMS PER LITER 

Injection dates

 October 25–26, 2004

Spring TI–SP (440243103193701)

Well DRU (440248103194501)

Figure 15. Rhodamine WT dye breakthrough curves for well DRU and spring TI–SP following dye injection 

in Rapid Creek, South Dakota, in 2004.

0

0.1

0.2

0.3

0.4

0.5

0 20 40 60 80 100 120 140 160 180

DAYS AFTER INJECTION AT SITE R1

RHODAMINE WT CONCENTRATION, IN MICROGRAM PER LITER 

Injection dates

 October 25–26, 2004

Spring JA–SP (440327103180501)

Concentration line of 0.06

 microgram per liter

Figure 16. Rhodamine WT dye concentrations for Jackson Springs gallery samples following injection in Rapid 

Creek, South Dakota, in 2004.

22 Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
0

5

15

10

25

20

35

30

40

0

0.5

1.5

1.0

2.5

2.0

3.5

3.0

4.0

6:00 8:00 10:00 12:00 14:00 16:00 18:00 20:00 22:00 24:00

TIME (October 26, 2004)

RHODAMINE WT CONCENTRATION FROM RAPID CREEK SITES,

IN MICROGRAMS PER LITER 

RHODAMINE WT CONCENTRATION FROM JACKSON SPRINGS GALLERY,

IN MICROGRAMS PER LITER 

Jackson Springs Gallery pumping rate

1,800

gallons/minute

3,100

gallons/minute

4,500

gallons/minute

EXPLANATION

Rapid Creek at

Braeburn Addition

(RC–BB)

Rapid Creek above

Cleghorn Springs

outfall (RC–AC)

Rapid Creek below

Cleghorn Springs

(RC–BC)

Jackson Springs

Gallery (JA–SP)

Figure 17. Time-series data of Rhodamine WT concentrations in samples from Rapid Creek sites and from Jackson Springs Gallery, 

Rapid Creek, South Dakota.

Analysis of Ground-Water Flow Paths and 

Velocities

The location of sites where fluorescein dye was detected 

following the Spring Creek dye injections (fig. 1) indicate a 

ground-water flow direction in the Madison aquifer that is 

east, then north from the streamflow loss zone. Dye breakthrough curves indicate conduit-dominated ground-water flow 

with this approximate orientation in the Spring Creek area. 

Well-defined flow paths were not identified in the Rapid Creek 

area east of the loss zone. Because of the few sampling sites 

and the complex ground-water flow system, potential flow 

paths could exist that were not identified in the study.

Spring Creek Area

The general direction of the flow path of dye from 

the Spring Creek loss zone is congruent with the flow path 

estimated by Long and Putnam (2002) (fig. 1). The transit 

times to downgradient wells in the Spring Creek area were 

consistent with an estimated transit time of 5 days for well HH 

(fig. 1) determined from the analysis of stable isotope timeseries data (Long and Putnam, 2004). Ground-water velocities 

calculated from the dye tracing ranged from about 770 to 

6,500 ft/d (table 6) for wells that were about 1 to 2 mi from the 

loss zone.

The dilution of fluorescein concentrations of about 

50 percent for well NON compared to the in-stream concentration for injection at site S1 over a 12-hour period indicates 

that a conduit directs ground-water flow to the northeast. 

The detection of dye in samples from wells north of Spring 

Creek is consistent with previous descriptions of a flow path 

directing Spring Creek recharge toward the Jackson-Cleghorn 

Springs complex described in Long and Putnam (2002, 2004). 

Preferential ground-water flow paths probably have been 

developed between the swallow holes in Spring Creek and 

Jackson-Cleghorn Springs. Although fluorescein dye was 

not detected at Jackson or Cleghorn Springs, the groundwater flow path appears to be oriented in that direction. A 

substantially larger amount of tracer dye may be required to 

be detected at these springs, if this is the endpoint of the flow 

path.

Comparison of dye breakthrough curves for well NON 

for injections at sites S1 and S4 (figs. 1 and 18) shows that 

the length of time that a solute would remain in the capture 

zone of well NON is almost an order of magnitude greater 

when streamflow recharge is receding than when streamflow 

Analysis of Ground-Water Flow Using Fluorescent Dyes 23
0

10

20

30

40

50

0 10 20 30 40 50 60 70 80

DAYS AFTER INJECTION

FLUORESCEIN CONCENTRATION, IN MICROGRAMS PER LITER 

2003 injection at site S1

2004 injection at site S4

Figure 18. Comparison of fluorescein dye breakthrough curves for well NON for 2003 and 

2004 injections in Spring Creek, South Dakota.

Table 6. Estimated ground-water velocities based on dye tracing for Spring Creek, South Dakota.

Sampling site 

(figure 1)

Dye injection site 

(figure 1)

Days to first 

arrival of dye

Distance from 

centroid of loss zone, 

in feet

Ground-water 

velocity, 

in feet per day

NON S1 1.6 10,400 6,500

NAY S1 2.5 9,400 3,760

CRO S1 7.8 12,200 1,564

NON S4 3.7 10,400 2,811

NAY S4 3.7 9,400 2,541

HH S4 2.1 9,400 4,476

CRO S4 15.9 12,200 767

CSN4 S4 14.7 15,200 1,034

24 Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
recharge in Spring Creek is near the loss threshold rate. The 

dye concentrations in samples from well NON remained 

greater than 10 μg/L for about 25 days following injection at 

site S4 in 2004 compared to about 2 days following injection 

at site S1 in 2003. Differences in recharge rates could 

substantially influence the transport of a potential contaminant 

introduced into the Spring Creek loss zone.

The differences in dye concentrations in samples from 

wells NAY and CSN4 for the four fluorescein dye injections 

(figs. 12 and 14) indicate that pumping schedules and 

streamflow recharge characteristics could have an important 

influence on solute transport to production wells that have 

indirect connections to the conduit. The data for well CSN4 

(figs. 12 and 14) indicate that when ground-water velocity 

in the conduit is high and pumping rates are low, solute 

concentrations could be small or not detectable. When the 

ground-water velocity in the conduit is slower and pumping 

rates are high, solute concentrations could be substantially 

larger.

Rapid Creek Area

A conduit flow path east of the loss zone was not 

evident from the dye injection in the Rapid Creek loss zone. 

Ground-water velocities in the Rapid Creek area could not 

be determined because the only two sites with detectable 

dye concentrations (fig. 7) were located within the loss 

zone. The number of wells available for sampling may 

have been inadequate to evaluate all potential flow paths. 

A potential explanation also could be dilution or dispersion 

of dye resulting from several factors. The thickness of the 

Madison Limestone in the Rapid Creek Canyon is about 316 ft 

compared to a thickness of 475 ft in Spring Creek Canyon 

(Miller, 2005). The thickness of the upper two units of the 

Madison Limestone described by Miller (2005) decreases 

from about 225 ft in Spring Creek Canyon to about 90 ft in 

Rapid Creek Canyon. The formation of conduits may be more 

likely in the upper two units than in the lower two units. The 

removal of the upper units by erosion may have resulted in a 

more diffuse network of solution openings in the Rapid Creek 

loss zone than in the Spring Creek loss zone. This is supported 

by Hines (1991), who indicated that the loss is more evenly 

distributed throughout the Rapid Creek loss zone.

Another potential factor is the relatively large and 

steady discharge from Jackson and Cleghorn Springs, which 

probably indicates the presence of many enlarged openings in 

the general area surrounding the springs. High transmissivity 

(40,000 feet squared per day) and large porosity in the 

Madison aquifer surrounding Jackson and Cleghorn Springs 

(Long and Putnam, 2002) may have caused greater dilution of 

dye than in other parts of the aquifer. Connections between the 

loss zone and the springs potentially could involve numerous 

smaller pathways with substantial dilution and mixing of the 

dye before discharge at Jackson or Cleghorn Springs.

Summary

The Madison aquifer, which is contained in the 

Mississippian-age Madison Limestone, is used extensively 

for water supplies for the city of Rapid City, S. Dak., and 

surrounding suburban communities. The 48-square-mile study 

area includes the west-central and southwest parts of Rapid 

City and the outcrops of the Madison Limestone extending 

from south of Spring Creek to north of Rapid Creek. The 

Madison Limestone is exposed on the western edge of the 

study area and dips to the east. An important component of 

recharge to the Madison Limestone is streamflow loss that 

occurs where streams cross the Madison Limestone outcrop 

(loss zone). The Madison Limestone, which is composed 

of limestone and dolostone, includes fractures and solution 

openings with karst features more prevalent in the upper parts 

than lower parts. The Spring Creek loss zone includes about 

2.3 river miles, and the maximum net loss rate is 21 cubic feet 

per second (ft3/s). The Rapid Creek loss zone includes about 

2.2 river miles, and the maximum net loss rate is 10 ft3/s. 

During 2003 and 2004, fluorescent dyes were injected in the 

Spring and Rapid Creek loss zones to estimate approximate 

loca­tions of preferential flow paths in the Madison aquifer and 

to mea­sure the response and transit times of a conservative 

tracer at wells and springs.

Four injections of about 2 kilograms of fluorescein dye 

at sites S1–S4 were made during 2003 and 2004 in the Spring 

Creek loss zone. Injection at site S1 on April 29, 2003, was 

made in streamflow just upstream from the loss zone over 

a 12-hour period when streamflow was about equal to the 

maximum loss rate. Injections at site S2 (May 22, 2003), site 

S3 (May 29, 2003), and site S4 (March 28, 2004) were in 

specific swallow holes located in the Spring Creek loss zone. 

Injection at site R1 (October 25–26, 2004) of 3.5 kilograms 

of Rhodamine WT dye was made in streamflow just upstream 

from the Rapid Creek loss zone over about a 28-hour period. 

Streamflow in Rapid Creek was about 21 ft3/s compared to a 

maximum loss rate of about 10 ft3/s; therefore, approximately 

50 percent of the injected dye was assumed to have moved into 

the Madison aquifer. A combination of 27 wells, 6 springs, 

and 3 stream sites were monitored with discrete samples 

following the injections.

For injections at sites S1–S3, when Spring Creek 

streamflow was greater than or equal to 20 ft3/s, fluorescein 

dye was detected in five wells that were located as many as 

about 2 miles from the loss zone, and time to first arrival 

ranged from less than 1 day to less than 10 days. The 

maximum concentration of 120 micrograms per liter (μg/L) 

at well CO, located adjacent to the loss zone, was similar to 

the concentration in the stream during injection at site S1. 

Following injection at site S1, dye arrived within 1.6 days 

at well NON, and the maximum concentration was 44 μg/L, 

which was about one-half the average stream concentration. 

For injection at site S4, when streamflow was about 12 ft3/s, 

Summary 25
Carter, J.M., and Redden, J.A., 1999c, Altitude of the top of 

the Deadwood Forma­tion in the Black Hills area, South 

Dakota: U.S. Geo­logical Survey Hydrologic Investigations 

Atlas HA–744–E, 2 sheets, scale 1:100,000.

Cattermole, J.M., 1969, Geologic map of the Rapid City 

west quadrangle, Pennington County, South Dakota: 

U.S. Geological Survey Geologic Quadrangle Map 

GQ–828, scale 1:24,000.

Driscoll, D.G., Hamade, G.R., and Kenner, S.J., 2000, 

Summary of precipitation data for the Black Hills area 

of South Dakota, water years 1931–98: U.S. Geological 

Survey Open-File Report 00–329, 163 p.

Ford, D.C., 1989, Features of the genesis of Jewel Cave 

and Wind Cave, Black Hills, South Dakota: National 

Speleological Society Bulletin, no. 51, p. 100–110.

Greene, E.A., 1993, Hydraulic properties of the Madison 

aquifer system in the western Rapid City area, South 

Dakota: U.S. Geological Survey Water-Resources 

Investigations Report 93–4008, 56 p.

Greene, E.A., 1999, Characterizing recharge to wells in 

carbonate aquifers using environmental and artificially 

recharged tracers, in Morganwalp, D.W., and Buxton, H.T., 

eds., Proceedings of the Technical Meeting, Charleston, 

S.C., March 8–12, 1999, Toxic Substances Hydrology 

Program: U.S. Geological Survey Water-Resources 

Investigations Report 99–4018-C, p. 803–808.

Greene, E.A., and Rahn, P.H., 1995, Localized anisotropic 

transmissivity in a karst aquifer: Ground Water, v. 33, no. 5, 

p. 806–816.

Gries, J.P., and Martin, J.E., 1985, Composite outcrop sec­tion 

of the Paleozoic and Mesozoic strata in the Black Hills and 

surrounding areas, in Rich, F.J., ed., Geology of the Black 

Hills, South Dakota and Wyoming (2d ed.): Field Trip 

Guidebook for the annual meeting of the Rocky Mountain 

Section of the Geological Society of America, Rapid City, 

S. Dak., April 1981, p. 261–292.

Hines, G.K., 1991, Ground-water and surface-water 

interaction in a reach of Rapid Creek near Rapid City, 

South Dakota: Rapid City, South Dakota School of Mines 

and Technology, unpublished M.S. thesis, 86 p.

Hortness, J.E., and Driscoll, D.G., 1998, Streamflow losses in 

the Black Hills of western South Dakota: U.S. Geo­logical 

Survey Water-Resources Investigations Report 98–4116, 

99 p.

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p. 7–16.

time to first arrival of dye at the same five wells ranged from 

0.2 to 16 days. Fluorescein dye also was detected at well 

CSN4 that was being used for water production in 2004; 

whereas, in 2003, this well was pumped only to collect 

samples. Following injection at site S4, the length of time that 

detectable dye remained in the capture zone of well NON, 

which is located approximately 2 miles from the loss zone, 

was almost an order of magnitude greater in 2004 than in 

2003.

For injection at site R1, dye was detected at well DRU 

and spring TI–SP with time to first arrival of about 0.5 day and 

1.1 days and maximum concentrations of 6.2 and 0.91 μg/L, 

respectively. Well DRU and spring TI–SP are located near 

the center of the Rapid Creek loss zone where there is a 

large meander in the creek. Measurable concentrations were 

observed for spring TI–SP as many as 109 days after the dye 

injection. Samples were collected from the Jackson Springs 

Gallery, which is located in the alluvium downstream from 

the loss zone along Rapid Creek, when dye was present in the 

stream. For the 16-hour period when samples were collected 

from the gallery at approximately 15-minute intervals, 

pumping from the gallery was incrementally increased from 

1,800 to 4,500 gallons per minute. After 10 hours at the high 

pumping rate, the Rhodamine WT concentrations in samples 

from the gallery increased from about 0.16 to 0.45 μg/L.

The direction of a conduit flow path in the Spring Creek 

area was to the northeast with ground-water velocities that 

ranged from 770 to 6,500 feet per day. A conduit flow path 

east of the loss zone was not evident from the dye injection in 

the Rapid Creek loss zone.

References Cited

Anderson, M.T., Driscoll, D.G., and Williamson, J.E., 1999, 

Ground-water and surface-water interaction along Rapid 

Creek near Rapid City, South Dakota: U.S. Geological 

Survey Water-Resources Investigation Report 98–4214, 

99 p.

Carter, J.M., Driscoll, D.G., Hamade, G.R., and Jarrell, G.J., 

2001, Hydrologic budgets for the Madison and Min­nelusa 

aquifers, Black Hills of South Dakota and Wyo­ming, water 

years 1987–96: U.S. Geological Survey Water-Resources 

Investigations Report 01–4119, 53 p.

Carter, J.M., and Redden, J.A., 1999a, Altitude of the top of 

the Minnelusa Formation in the Black Hills area, South 

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of the Madison Limestone in the Black Hills area, South 

Dakota: U.S. Geological Survey Hydrologic Investigations 

Atlas HA–744–D, 2 sheets, scale 1:100,000.

26  Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04
Jones, W.K., 1984, Dye tracer tests in karst areas: National 

Speleological Society Bulletin v. 46, no. 2, p. 3–9.

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the Madison and Minnelusa aquifers in the Rapid City area, 

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stratigraphy on ground-water flow paths in the karstic 

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Ph.D. dissertation, 191 p.

Naus, C.A., Driscoll, D.G., and Carter, J.M., 2001, 

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Rahn, P.H., 1971, The hydrologic significance of the 

November, 1986 dye test on Boxelder Creek, Black Hills, 

South Dakota: Proceedings, South Dakota Academy of 

Science, v. 50, p. 52–56.

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Black Hills, South Dakota and Wyoming: South Dakota 

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units in the Black Hills area, South Dakota: U.S. Geological 

Survey Hydrologic Investigations Atlas HA–743, 3 sheets, 

scale 1:100,000.

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Dakota, water year 2003: U.S. Geological Survey WaterData Report SD–03–1 (published annually).

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Dakota, water year 2004: U.S. Geological Survey WaterData Report SD–04–1 (published annually).

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procedures for dye tracing: U.S. Geological Survey 

Techniques of Water-Resources Investigations, book 3, 

chap. A12, 34 p.

References Cited 27
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Manuscript approved for publication, July 10, 2007.

Prepared by the Helena Publishing Service Center.

For more information concerning the research in this report, contact:

 U.S. Geological Survey

 Director, South Dakota Water Science Center

 1608 Mountain View Road

 Rapid City, SD 57702

 http://sd.water.usgs.gov/
Putnam and Long—Analysis of Ground-Water Flow in the Madison Aquifer using Fluorescent Dyes near Rapid City, South Dakota, 2003–04—SIR 2007–5137

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