Geologic, Hydraulic, and 

Geochemical Controls

on Fate, Transport, and 

Remediation of VOCs

USEPA-USGS Fractured Rock Workshop

EPA Region 2

14 January 2014

Allen M. Shapiro, USGS
Controls on Fate, Transport, and Remediation of VOCs 2

Diversity of Fractured Rock Aquifers 

Granite and schist

Mirror Lake, NH

Madison Limestone, 

Rapid City, SD Biscayne Limestone, 

Ft. Lauderdale, FL

Lockatong

Mudstone,

West Trenton, 

NJ

Tonalite, 

Washington, DC

Silurian Dolomite

Argonne, IL

Sykesville Gneiss,

Washington, DC
 Fractured rock aquifers are highly diverse

 . . .however. . .all fractured rock aquifers share 

similar physical attributes

 Similar attributes provide for. . .

 Generic discussion of physical and chemical 

transport processes

 Standardized approaches to characterization and 

monitoring

 Design and application of diagnostic and modeling 

tools

 Expect site specific complexities

Diversity of Fractured Rock Aquifers

Controls on Fate, Transport, and Remediation of VOCs 3
Sand and gravel, glacial outwash

Cape Cod, Massachusetts

Schematic of 

intergranular void 

space in an 

unconsolidated 

sand

Length-to-width ratio of void space ~1

Heterogeneous nature of 

geologic materials is 

limited. . .direction of 

groundwater flow can be 

readily identified from the 

hydraulic gradient. . . 

“Pore” scale variability in fluid 

velocity (magnitude and direction) 

results in spreading of a chemical 

constituent. . .

Groundwater flow

Chemical transport

Controls on Fate, Transport, and Remediation of VOCs 4

Expectations for unconsolidated porous media

Similar interpretations of groundwater flow and chemical transport cannot be applied to fractured rock aquifers 

because of unique physical attributes of fractured rock. . . 

Dimensions of the void space are small 

relative to scale of the problem of interest 

(groundwater flow, chemical transport)
Expectations of fractured rock: Hierarchy of void space

Controls on Fate, Transport, and Remediation of VOCs 5

Iron-hydroxide 

precipitate staining 

the rock matrix 

(primary/intrinsic 

rock porosity)

Fractures exposed on a road cut 

(fracture porosity)

Fault zone exposed 

on a road cut

Granite and schist, Mirror Lake Watershed

Grafton County, New Hampshire

Residual wetting of rock core 

(primary/intrinsic rock 

porosity)

Fractures parallel and perpendicular 

to bedding (fracture porosity)

Schematic cross section 

perpendicular to bedding

showing fault zone location

Lockatong Mudstone, Newark Basin

West Trenton, New Jersey
Controls on Fate, Transport, and Remediation of VOCs 6

Expectations of fractured rock: Large variability in 

capacity to transmit 

groundwater
Borehole H1

Mirror Lake Watershed, NH

Granite and Schist

Packer apparatus 

used for testing 

individual or closely 

spaced fractures

Shapiro and Hsieh, 1998; Shapiro et al., 2007 

Expect both vertical and horizontal variability. . . 

Controls on Fate, Transport, and Remediation of VOCs 7

Expectations of fractured rock:

K of the intrinsic rock (matrix) porosity is orders of 

magnitude less than that of fractures

Abrupt spatial changes 

in hydraulic properties
Local and regional stress distribution, lithology, and weathering lead to complex connectivity of 

fractures and their hydraulic properties. . . 

Boundary

Iron staining No staining

Schist: fewer fractures; 

longer, undulating fracture 

surfaces 

Granite: higher fracture 

density; shorter, more 

planar fractures

Controls on Fate, Transport, and Remediation of VOCs 8

Combination of large variation in K coupled with 

complex fracture connectivity = convoluted 

groundwater flow paths

Expectations of fractured rock: Complex fracture 

connectivity

Bedding plane parting along 

black, carbon-rich section of 

mudstone

Joints perpendicular to bedding 

(parallel and perpendicular to 

rock face)

Fracture density 

perpendicular to 

bedding varies with 

proximity to fault

Granite and 

schist, Mirror 

Lake 

Watershed

Grafton 

County, New 

Hampshire

Lockatong Mudstone, Newark Basin

West Trenton, New Jersey
Fracture surfaces have complex topology. . .fracture aperture varies due to points of contact and 

asperities between fracture walls

. . .similar to the large variability in hydraulic properties that is anticipated from one fracture to the 

next, there is large variability in hydraulic properties within an individual fracture. . .

Neretnieks et al., 1982; Tsang and Neretnieks 1998

Controls on Fate, Transport, and Remediation of VOCs 9

Convoluted groundwater flow paths within individual fractures

Expectations of fractured rock: Fracture surfaces have 

complex topology
What’s important ?

How do we approach this level of complexity for site- and 

regional-scale investigations? 

• Identify lithologic and geomechanical controls

• Identify most permeable features and barriers to 

groundwater flow over relevant dimensions

• Spatial connectivity of permeable features

• Mapping and characterization of every fracture is not

warranted

• Variability within an individual fracture is below our 

resolution capacity*

Controls on Fate, Transport, and Remediation of VOCs 10

Expectations: Convoluted groundwater flow paths 

over dimensions from meters to kilometers. . . 
Characterizing fluid advection and the migration of aqueous phase contaminants. . .monitoring hydraulic head in 

discrete intervals of boreholes 

Controls on Fate, Transport, and Remediation of VOCs 11

Consequences of Complexity in Fractured Rock:

Characterizing hydraulic head is a 3-D concept. The direction of groundwater flow must be inferred 

in concert with the characterization of permeable features and flow barriers. 

Characterizing the direction of groundwater flow 
Characterizing fluid advection and the migration of aqueous phase contaminants. . .monitoring hydraulic head in 

discrete intervals of boreholes 

Controls on Fate, Transport, and Remediation of VOCs 12

Consequences of Complexity in Fractured Rock:

Characterizing the direction of groundwater flow 

Maintaining the integrity of multilevel monitoring equipment. . . proper monitoring of hydraulic 

head is critical to inferring directions of groundwater flow.
Borehole H1, Granite and Schist, Mirror Lake Watershed, NH

Monitoring geochemical conditions 

in fractured rock. . .boreholes open 

to multiple fractures. . . 

Pumping. . .mixing contributions 

from multiple fractures . . .

Pumping. . .groundwater drawn 

preferentially from most 

transmissive fractures. . .

Controls on Fate, Transport, and Remediation of VOCs 13

Consequences of Complexity in Fractured Rock:

Characterizing the distribution of contaminants
Naval Air Warfare Center, West Trenton, NJ, Lockatong Mudstone, Newark Basin

TCE concentration (36BR open interval): 

102 – 125 ft below land surface = 89,000 g/L

TCE concentration (36BR interval A): 

102 – 112 ft below land surface = 19,000 g/L

Controls on Fate, Transport, and Remediation of VOCs 14

Consequences of Complexity in Fractured Rock:

Characterizing the distribution of contaminants

Transmissivity of 36BR – interval A (102 – 112 ft below land surface) – 1.0 x 10-5 m2/s 

Transmissivity of 36BR – interval B (112 – 125 ft below land surface) – 1.0 x 10-7 m2/s 

Flux averaged concentration: CAx (1.00/1.01) + CBx (0.01/1.01) = Copenhole

CA = 19,000 g/L

Copenhole = 89,000 g/L

CB > 1,000,000 g/L
DNAPLs in geologic media

DNAPL pooling at a 

boundary between larger 

beads [0.85 – 1.23 mm] 

(upper region) and 

smaller beads [0.49 –

0.70 mm] (lower region) 

Schwille 1988

Complex DNAPL 

migration in 

unsaturated sands. 

DNAPL shown in red 

(Sudan IV dye). 

Bedding dips 30o

below horizontal 

15 cm

Poulsen and Kueper, 1992

• Capillary forces define the distribution of DNAPLs

• Complex spatial distribution of DNAPLs (both vertically and 

laterally) from minor variations in pore space geometry

• DNAPLs at great depths - density > groundwater

• DNAPL “pool” heights force DNAPL into small pore throats; 

hydraulic conditions may not be capable of removing DNAPL from 

small pore throats

• Pumping and drilling may re-mobilize “pools” of DNAPL

• DNAPLs dissolve into groundwater

• Dissolved-phase DNAPLs diffuse into lower-permeability geologic 

materials 

• VOCs sorb to geologic materials with organic content

Controls on Fate, Transport, and Remediation of VOCs 15

Consequences of Complexity in Fractured Rock:

Complex spatial distribution of contaminants
Complex topology of fractures affects contaminant distribution. . .

Entry of DNAPLs into fractures depends on physical properties of fractures and the DNAPL,

and capillary forces. . . 

Kueper and McWhorter, 1992; 

Kueper et al., 2003

Controls on Fate, Transport, and Remediation of VOCs 16

Consequences of Complexity in Fractured Rock:

Complex spatial distribution of contaminants
Fracture aperture affects contaminant distribution. . .

•For a given “pool height” of DNAPL, fractures to the right of these curves would allow 

entry of DNAPL

•9 micron (9 x 10-6 meters) fracture aperture needed to stop 1 meter “pool” height of TCE

•Diameter of human hair ~50 microns

Kueper and McWhorter, 1992; Kueper et al., 2003

Controls on Fate, Transport, and Remediation of VOCs 17

Consequences of Complexity in Fractured Rock:

Complex spatial distribution of contaminants
Retention and slow release 

of contaminants in “flow 

limited” regions of the 

aquifer. . .a significant 

impediment to achieving 

remedial objectives in a 

reasonable time frame. . . 

from Doner and Sale, Colorado State University 

Low-permeability material embedded in a permeable sand. . . 

Dye injection. . . 

Controls on Fate, Transport, and Remediation of VOCs 18

Consequences of Complexity in Fractured Rock:

Significance of “flow limited” regions of the aquifer

Flushing. . . 

• Low permeability 

material may not be 

significant with respect 

to volumetric 

groundwater flow. . . 

• During contaminant 

“loading”, dye diffuses 

from permeable 

pathways to lowpermeability materials 

due to concentration 

gradient

• During “flushing”, dye 

diffuses from lowpermeability materials to 

permeable pathways due 

to concentration gradient
The primary/intrinsic porosity of the rock (rock matrix) offers a fluid-filled void space available to 

chemical constituents . . .

Wood et al., 1996

Frequency histogram of porosity in rock types of the 

Mirror Lake Watershed, New Hampshire

Iron hydroxide staining on fracture 

surfaces and in the rock matrix. . .oxygen 

diffusing into the rock matrix and reacting 

with dissolved iron

Controls on Fate, Transport, and Remediation of VOCs 19

Consequences of Complexity in Fractured Rock:

Significance of “flow limited” regions of the aquifer
Lockatong Mudstone

Naval Air Warfare Center, West Trenton, NJ

Depth where DNAPL 

detected during 

coring

Detection limit 

for TCE in 

groundwater 

samples is 1 g/L

Controls on Fate, Transport, and Remediation of VOCs 20

Consequences of Complexity in Fractured Rock:

Significance of “flow limited” regions of the aquifer

D

e

pth (fe

et b

elo

w lan

d surface)

Sandstone

Simi Hills, Ventura County, California

Monitoring 

interval #6

Monitoring 

interval #3

Sterling et al., 2005

Multilevel

monitoring

Jan 1998
Matrix Diffusion in Fractured Rock

100 meters

2

5

m

eters

Vertical exaggeration x 4

Log10 (C/Co)

-25 -20 -15 -10 -5 0

Fracture

(v = 100 m/yr)

Rock matrix

C = Co (0 < t < 10 years)

C = 0 (t > 10 years)
Matrix Diffusion in Fractured Rock

100 meters

2

5

m

eters

Vertical exaggeration x 4

Log10 (C/Co)

-25 -20 -15 -10 -5 0

Fracture

(v = 100 m/yr)

Rock matrix

C = Co (0 < t < 10 years)

C = 0 (t > 10 years)

-1

-3

-10

-15

-5

-20

elapsed time = 10 years
Matrix Diffusion in Fractured Rock

100 meters

2

5

m

eters

Vertical exaggeration x 4

Log10 (C/Co)

-25 -20 -15 -10 -5 0

Fracture

(v = 100 m/yr)

Rock matrix

C = Co (0 < t < 10 years)

C = 0 (t > 10 years)

-3

-1

-1

-3

-10

-15

-5

elapsed time = 20 years
Matrix Diffusion in Fractured Rock

100 meters

2

5

m

eters

Vertical exaggeration x 4

Log10 (C/Co)

-25 -20 -15 -10 -5 0

Fracture

(v = 100 m/yr)

Rock matrix

C = Co (0 < t < 10 years)

C = 0 (t > 10 years)

-5

-3

-3

-10

-1

-1

elapsed time = 30 years
Matrix Diffusion in Fractured Rock

100 meters

2

5

m

eters

Vertical exaggeration x 4

Log10 (C/Co)

-25 -20 -15 -10 -5 0

C = Co (0 < t < 10 years)

C = 0 (t > 10 years)

-5

-3

-3

elapsed time = 50 years

Concentration gradient 

driving contaminant mass 

toward the fracture. . .

Concentration gradient 

driving contaminant mass 

away from the fracture. . 

Over time, concentration 

gradient toward fracture 

decreases. . . reducing 

mass flux to the fracture. 
Controls on Fate, Transport, and Remediation of VOCs 26

Consequences of Complexity in Fractured Rock:

Matrix diffusion. . .a curse or a blessing ?

the curse. . .retention of contaminants in flow limited 

regions of the aquifer. . .limiting access to remediation 

amendments. . .slow release of contaminants to permeable 

pathways yields a long-term contaminant source. . . 

An example: Pulse injection and monitoring 50 m downgradient

the blessing. . .retention of contaminants in flow 

limited regions of the aquifer. . .delaying 

downgradient migration of contaminants. . 

.attenuating the downgradient concentrations. . . 

. . .matrix diffusion is the rationale for the licensing 

of selected geologic environments as sites for 

waste isolation (e.g., WIPP site, New Mexico, USA) 
Lockatong Mudstone

Naval Air Warfare Center, West Trenton, NJ

Controls on Fate, Transport, and Remediation of VOCs 27

Consequences of Complexity in Fractured Rock:

Other processes in “flow limited” regions of the aquifer

Sharp concentration gradients in the 

rock matrix adjacent to fractures. . . 

Over time, diffusion tends to 

diminish sharp concentration 

gradients. . . 

Retention and release of 

contaminants also controlled by 

surface processes 

(sorption/desorption) on fracture 

surfaces and in the rock matrix. . .

Organic contaminants (e.g., TCE) 

have a surface affinity for organic 

materials (e.g., organic carbon)

Sorption/desorption changes 

dynamics for retention and release 

of contaminants
Naval Air Warfare Center, West Trenton, NJ

Isocontours of TCE concentration 

at 100 ft below land surface

Mudstone units of the Lockatong Fromation

on Cross Section G – G’

G

G’

F

F’ 100 ft below 

land surface

Interpreting contaminant distribution based on water 

samples collected from short (~20 ft) intervals open in a 

fractured mudstone. . .

Controls on Fate, Transport, and Remediation of VOCs 28

Consequences of Complexity in Fractured Rock:

Interpreting the spatial distribution of contaminants

Lacombe 2011

Interpretation of concentrations in mobile groundwater 

(fractures). . .does not necessarily reflect total in situ 

contaminant mass. . . 
How do we approach this level of complexity for site- and 

regional-scale investigations? 

• “Classical” (Gaussian-shaped) plumes are unlikely

• Differentiate between contaminants in mobile and 

immobile (flow-limited) regions of the aquifer

• Quantify contaminant mass in flow-limited regions of the 

aquifer. . . the rock matrix may retain significant 

contaminant mass (aqueous chemical diffusion and 

surface processes)

• Grasp the significance of residence times and mass 

exchange between fractures and the rock matrix

Controls on Fate, Transport, and Remediation of VOCs 29

What’s important ?

Expectations: Complex spatial distribution of 

contaminants in fractures and the rock matrix. . . 
Final Thoughts

Controls on Fate, Transport, and Remediation of VOCs 30

Keep in mind. . .fractured rock aquifers have similar physical 

attributes. . .as well as site specific complexities. . . 

These (similar) attributes are the starting point for the 

development of Conceptual Site Models. . .a conceptual 

understanding of the hydrogeologic and biogeochemical controls 

on groundwater flow and contaminant fate and transport. . .site 

specific complexities are needed to fill in the details. . . 

These (similar) attributes need to be recognized in 

characterization, monitoring, and modeling at fractured rock 

sites. . .