Master of Science / Department of Geology / Saugata Datta / In specific lithologic and hydrogeological settings, Managed Aquifer Recharge (MAR) projects using vadose zone wells have the potential to outperform infiltration basins in terms of volume of water recharged. Numerical modeling can assist in determining which recharge method is most efficient in infiltrating water to unconfined alluvial aquifers of differing unsaturated zone lithologic complexities. The Sagamore Lens Aquifer (SLA) in Cape Cod, Massachusetts is an example of an aquifer with minimal lithologic complexity while the Hueco Bolson Aquifer (HBA) near El Paso, Texas has greater lithologic complexity. This research combines two U.S. Geological Survey numerical models to simulate recharge from infiltration basins and vadose wells at these two locations. VS2DTI, a vadose zone model, and MODFLOW-2005, a saturated zone model, were run sequentially at both sites and with both vadose well and infiltration basin recharge methods simulated. Results were compared to determine the relative effectiveness of each method at each location and to determine the effects of vadose zone complexity on recharge. At the HBA location, soil samples were tested for conductivity and grain size distribution and a microgravity survey was begun to constrain the models. The infiltration basin structure proved to be more efficient, infiltrating more water volume at both locations. Lithologic complexity formed perched conditions in the HBA model, significantly affecting infiltration rates from both infiltration methods at that location. Methods and conclusion from this study can assist in the modeling and design of future MAR projects, especially in locations with thick or lithologically complex vadose zones.

The impact of the soil structure on flow and transport in partially water saturated soils is currently still a matter of scientific debate. The major aim of this thesis was to investigate the relation between heterogeneity and transport for a natural unsaturated heterogeneous Tertiary sand deposit. In the first part, we analyzed the flow and transport at the scale of an undisturbed monolith. Chloride breakthrough curve experiments were used to derive an apparent dispersion coefficient at the TDR sampling and monolith scale. Application of a Brilliant Blue pulse allowed further the visualization of flow distribution within the monolith. Small undisturbed soil cores were sampled throughout the monolith and the hydraulic characteristic curves at the scale of the cores were determined. Textural variability and structure as inferred from the inspection of the Brilliant Blue pattern and analysis of the small core sampling were subsequently implemented in a 3-D model and transport was simulated. The simulations clearly revealed the importance of the macro-structure on the transport behavior of the soil. We also showed that the micro-variability heterogeneity component was needed to assess the scaling of the effective and local scale dispersivity. In the second part, we studied in-situ chloride transport in the vadose formation separating the bottom of a lake and an unconfined aquifer. First the uncertainty generated by the undersampling of the lake chloride concentration time series were investigated. Subsequently, velocity and dispersivity profiles were assessed by inverse modeling of the soil chloride concentration time series. We observed that the clay layers induced an increase of the dispersivity below them. We hypothesize that fingering flow or convergence phenomena, occurring below sand-clay interfaces, lead to non-representative artificially high dispersivity values. Velocity and dispersivity values just above the clay layers however seem more reliable due to convergence phenomena and better lateral mixing induced by a larger water content. In this formation, the transport behavior could be characterized considering a hierarchical structure of the subsoil heterogeneity. In this model, the flow field micro-variability is influenced by pore structure (possibly characterized by scaling factors). The next complexity level is induced by the slight layering resulting from the sedimentation process (not investigated in this work). Then, the third hierarchical level is assessed by the macro-structure and the sequence of clay layers in the sand. Each of these levels is assumed to have an effect on the solute mixing process and effective macro-dispersivity.

No / This is the second in a series of three papers from a project that has attempted to answer the question ‘does the application of agrochemicals accelerate the corrosion of archaeological metals in the top 50cm of the soil?’. We have approached it through a combination of field-based experiments, by establishing laboratory microcosms and by using geochemical modelling techniques to understand the processes involved. This paper reports on two different experimental approaches in the laboratory - a microcosm designed to mimic one of the burial sites (the ‘Lab Bin’ experiments), and a simpler one to understand the reaction between metal samples and concentrated aqueous solutions of the fertilizers and laboratory reagents used (the ‘Lab Beaker’ experiments). The bins were monitored for in situ corrosion and aqueous effluent collected for13 weeks, after which they were excavated and the metal coupons examined. The Lab Beakers were monitored for in situ corrosion for seven weeks, and then the coupons examined. We focus here on a sub-set of the data relating to the behaviour of the thinnest samples of copper in each case. As with the field data previously reported, the results are sometimes contradictory, but on balance this project has demonstrated that applied agricultural chemicals are likely to accelerate the rate of corrosion of metal objects within 50cm of the surface. In particular, it is likely that any fertilizers containing KCI will be particularly aggressive.

No / This is the third in a series of papers from a pilot project that has attempted to answer the question ‘does the application of agrochemicals accelerate the corrosion of archaeological metals in the top 50cm of the soil?’. We have approached it by a combination of field-based experiments, by establishing laboratory microcosms and by using geochemical modeling techniques to understand the processes involved. This paper reports on the geochemical modelling simulations that trace the potential corrosion pathways followed in two sets of laboratory microcosm experiments (‘Lab Beakers’ and ‘Lab Bins’) and one field experiment (at Palace Leas). This approach uses soil solution as the fluid mediating corrosion in the soil vadose zone. Soil solution was displaced following controlled exposure to fertilizers. Modelling using The Geochemists Workbench was carried out to mimic the experimental conditions, and predictions were compared with image analysis results, limited XRD analysis and published corrosion observations. We focus here on a sub-set of the data relating to the behaviour of the thinnest samples of copper in each case. As with the field and laboratory data previously reported, the results are sometimes contradictory, but on balance this project has demonstrated that applied agricultural chemicals are likely to accelerate the rate of corrosion of metal objects within 50cm of the surface. In particular, it is likely that any fertilizers containing KCI (‘potash’) will be particularly aggressive. Geochemical modeling generates plausible corrosion predictions based on post-depositional interaction between archaeological copper and soil solution, and appears to be useful in helping to simplify and understand corrosion pathways in naturally complex systems.

No / Part of a project that has attempted to answer the question ‘does the application of agrochemicals accelerate the corrosion of metals in the top 50cm of the soil? ’ is reported. We have approached the question by a combination of field-based experiments (on two sites), establishing laboratory microcosms (one involving simple aqueous systems and the other a series of simulated burial experiments) and by using geochemical modelling techniques to understand the processes involved. Two different experimental approaches in the field are documented — one using in situ monitoring of corrosion potentials and the other assessing the degree of induced corrosion using image analysis on recovered samples. The first was carried out on arable land close to the University of Bradford to which we applied different fertilizer regimes. The second was established on land owned by the University of Newcastle at Palace Leas, Morpeth, Northumberland, which has a documented field management regime extending back over one hundred years. We focus here on a sub-set of the data relating to the behaviour of the thinnest samples of copper in each case. There does seem to be some evidence of an effect resulting from the applied fertilizer, but the data are sometimes contradictory. We suggest a number of improvements for future field experiments that monitor in situ corrosion in the vadose zone.

Characterization of heterogeneous soil hydraulic parameters of deep vadose zones is often difficult and expensive, making it necessary to rely on other sources of information. Pedotransfer functions (PTFs) based on soil texture data constitute a simple alternative to inverse hydraulic parameter estimation, but their accuracy is often modest. Inverse modeling entails a compromise between detailed description of subsurface heterogeneity and the need to restrict the number of parameters. We propose two methods of parameterizing vadose zone hydraulic properties using a combination of k-means clustering of kriged soil texture data, PTFs, and model inversion. One approach entails homogeneous and the other heterogeneous clusters. Clusters may include subdomains of the computational grid that need not be contiguous in space. The first approach homogenizes within-cluster variability into initial hydraulic parameter estimates that are subsequently optimized by inversion. The second approach maintains heterogeneity through multiplication of each spatially varying initial hydraulic parameter by a scale factor, estimated a posteriori through inversion. This allows preserving heterogeneity without introducing a large number of adjustable parameters. We use each approach to simulate a 95 day infiltration experiment in unsaturated layered sediments at a semiarid site near Phoenix, Arizona, over an area of 50 x 50 m(2) down to a depth of 14.5 m. Results show that both clustering approaches improve simulated moisture contents considerably in comparison to those based solely on PTF estimates. Our calibrated models are validated against data from a subsequent 295 day infiltration experiment at the site.

Biogeochemical reactions and vadose zone transport, in particular gas phase transport, are inherently coupled processes. To explore feedback mechanisms between these processes in a quantitative manner, multicomponent gas diffusion and advection are implemented into an existing reactive transport model that includes a full suite of geochemical reactions. Multicomponent gas diffusion is described based on the Dusty Gas Model, which provides the most generally applicable description for gas diffusion. Gas advection is described by Darcy's Law, which in the current formulation, is directly substituted into the transport equations. The model is used to investigate the interactions between geochemical reactions and transport processes with an emphasis to quantify reaction-induced gas migration in the vadose zone. Simulations of pyrite oxidation in mine tailings, gas attenuation in partially saturated landfill soil covers, and methane production and oxidation in aquifers contaminated by organic compounds demonstrate how biogeochemical reactions drive diffusive and advective transport of reactive and non-reactive gases. Pyrite oxidation in mine tailings causes a pressure reduction in the reaction zone and drives advective gas flow into the sediment column, enhancing the oxidation process. Release of carbon dioxide by carbonate mineral dissolution partly offsets pressure reduction, and illustrates the role of water-rock interaction on gas transport. Microbially mediated methane oxidation in landfill covers reduces the existing upward pressure gradient, thereby decreasing the contribution of advective methane emissions to the atmosphere and enhancing the net flux of atmospheric oxygen into the soil column. At an oil spill site, both generation of CH4 in the methanogenic zone and oxidation of CH4 in the methanotrophic zone contribute to drive advective and diffusive fluxes. The model confirmed that non-reactive gases tend to accumulate in zones of gas consumption and become depleted in zones of gas production. In most cases, the model was able to quantify existing conceptual models, but also proved useful to identify data gaps, sensitivity, and inconsistencies in conceptual models. The formulation of the model is general and can be applied to other vadose zone systems in which reaction-induced gas transport is of importance.

Near-surface sediments play an important role in governing the movement of water and contaminants from the land surface through the vadose zone to groundwater. Generally, low permeability surficial soils restrict water flow through the vadose zone and form a natural protective barrier to migration of surface applied contaminants. These types of fine-grained soils commonly contain macropores, such as fractures, animal burrows, and root holes, that have been identified as preferential flow pathways in the subsurface. Accordingly, macropores have the potential to influence groundwater recharge rates and compromise the protective capacity of surficial soils, particularly where the overburden is thin and aquifers are close to the surface. Partially saturated flow and transport in these environments is inherently complex and not well understood. The objective of this thesis was to examine preferential flow processes and the associated movement of contaminants in macroporous, low permeability soils. This was accomplished by conducting numerical and field experiments to investigate and describe the dynamics of macropore flow during episodic infiltration through the vadose zone and evaluate the corresponding influence of macropores on vertical water flow and contaminant transport. Numerical simulations were conducted to identify the important physical factors controlling flow and transport behaviour in partially saturated, fractured soils. A three-dimensional discrete fracture model, HydroGeoSphere, was used to simulate infiltration into homogeneous soil blocks containing a single vertical rough-walled fracture. Relatively large rainfall events with return periods ranging from 5 to 100 years were used, since they are more likely to generate significant preferential flow. Initial results showed that flow system dynamics were considerably more sensitive to matrix properties, namely permeability and antecedent moisture content, than fracture properties. Capillary forces, combined with the larger water storage capacity in the soil matrix, resulted in significant fracture-matrix interaction which effectively limited preferential flow down the fracture. It is also believed that fracture-matrix interaction reduced the influence of fracture roughness and other related small-scale fracture properties. The results imply that aperture variability within individual fractures may be neglected when modeling water flow through unsaturated soils. Nevertheless, fracture flow was still an important process since the fracture carried the majority of the water flow and virtually all of the mass of a surface applied tracer to depth in the soil profile. Model runs designed to assess transport variability under a variety of different physical settings, including a wider range of soil types, were also completed. Vertical contaminant fluxes were examined at several depths in the soil profile. The results showed that the presence of macropores (in the form of fractures) was more important than matrix permeability in controlling the rate of contaminant migration through soils. The depth of contaminant migration was strongly dependent on the antecedent moisture content and the presence of vertically connected fractures. Soil moisture content played a pivotal role in determining the onset and extent of preferential flow, with initially wet soils much more prone to macropore flow and deep contaminant migration. Simulations showed that surface applied tracers were able to reach the base of 2 m thick fractured soil profiles under wetter soil conditions (i.e., shallow water table). Likewise, long-duration, low-intensity rainfall events that caused the soil to wet up more resulted in proportionately more contaminant flux at depth. Fractured soils were particularly susceptible to rapid colloid movement with particle travel times to depths of 2 m on the order of minutes. The main implication is that the vulnerability of shallow groundwater is related more to vertical macropore continuity and moisture conditions in the soil profile, rather than traditional factors such as soil thickness and permeability. Macropore flow and transport processes under field conditions were investigated using small-scale infiltration experiments at sites in Elora and Walkerton, Ontario. A series of equal-volume infiltration experiments were conducted at both sites using a tension infiltrometer (TI) to control the (negative) infiltration pressures and hence the potential for macropore flow. A simulated rainfall experiment was also conducted on a small plot at Walkerton for comparison with the TI tests. Brilliant Blue FCF dye and fluorescent microsphere tracers were applied in all tests as surrogates for dissolved and colloidal contaminant species, respectively. Upon completion of infiltration, excavations were completed to examine and photograph the dye-stained flow patterns, map soil and macropore features, and collect soil samples for analysis of microspheres. Cylindrical macropores, in the form of earthworm burrows, were the most prevalent macropore type at both sites. In the TI tests, there was a clear relationship between the vertical extent of infiltration and the maximum pressure head applied to the TI disc. Larger infiltration pressures resulted in increased infiltration rates, more spatial and temporal variability in soil water content, and increased depths of dye penetration, all of which were attributed to preferential flow along macropores. Preferential flow was limited to tests with applied pressure heads greater than -3 cm. Under the largest applied pressures (greater than -1.0 cm), dye staining was observed between 0.7 and 1.0 m depth, which is near the seasonal maximum water table depth at both field sites. The tension infiltrometer was also used to infiltrate dye along an exposed vertical soil face, thereby providing a rare opportunity to directly observe transient macropore flow processes. The resulting vertical flow velocities within the macropores were on the order of tens of meters per day, illustrating the potential for rapid subsurface flow in macropores, even under partially saturated conditions. The results suggest that significant flow occurred in partially saturated macropores and this was supported by simple calculations using recent liquid configuration models for describing flow in idealized macropores. On all excavated sections, microspheres were preferentially retained (relative to the dye) in the top five centimeters of the soil profile. Below this zone, dye patterns correlated well with the presence of microspheres in the soil samples. There was evidence for increased retention of microspheres at lower water contents as well as a slightly greater extent of transport for smaller microspheres. In general, the microsphere and dye distributions were clearly dictated by vadose zone flow processes. As in the numerical experiments, water storage in the soil matrix and related macropore-matrix interaction were important factors. Mass transfer of water through the macropore walls promoted flow initiation in the macropores near surface. Deeper in the soil, water drawn away from the macropores into the matrix significantly retarded the downward movement of water along the macropores. Imbibition of dye from the macropores into the matrix was repeatedly observed on excavated soil sections and during the transient dye test. Microspheres were also transported laterally into the soil matrix indicating that conceptual models for colloid transport in the vadose zone need to account for this mass transfer process. Overall, the tension infiltrometer performed extremely well as a tool for controlling macropore flow under field conditions and, together with the dye and microsphere tracers, provided unique and valuable insights into small-scale flow and transport behavior. The field experiments raise concerns about the vulnerability of shallow groundwater in regions with thin, macroporous soils. Only a fraction of the visible macropores contributed to flow and transport at depths greater than 40 cm. However, with dye and microsphere transport observed to more than 1.0 m depth, rapid macropore flow velocities, and the sheer number of macropores present, there was clearly potential for significant flow and transport to depth via macropores. Under the right conditions, it is reasonable to speculate that macropores may represent a significant pathway for migration of surface applied contaminants to groundwater over the course of a single rainfall event.

Near-surface sediments play an important role in governing the movement of water and contaminants from the land surface through the vadose zone to groundwater. Generally, low permeability surficial soils restrict water flow through the vadose zone and form a natural protective barrier to migration of surface applied contaminants. These types of fine-grained soils commonly contain macropores, such as fractures, animal burrows, and root holes, that have been identified as preferential flow pathways in the subsurface. Accordingly, macropores have the potential to influence groundwater recharge rates and compromise the protective capacity of surficial soils, particularly where the overburden is thin and aquifers are close to the surface. Partially saturated flow and transport in these environments is inherently complex and not well understood. The objective of this thesis was to examine preferential flow processes and the associated movement of contaminants in macroporous, low permeability soils. This was accomplished by conducting numerical and field experiments to investigate and describe the dynamics of macropore flow during episodic infiltration through the vadose zone and evaluate the corresponding influence of macropores on vertical water flow and contaminant transport. Numerical simulations were conducted to identify the important physical factors controlling flow and transport behaviour in partially saturated, fractured soils. A three-dimensional discrete fracture model, HydroGeoSphere, was used to simulate infiltration into homogeneous soil blocks containing a single vertical rough-walled fracture. Relatively large rainfall events with return periods ranging from 5 to 100 years were used, since they are more likely to generate significant preferential flow. Initial results showed that flow system dynamics were considerably more sensitive to matrix properties, namely permeability and antecedent moisture content, than fracture properties. Capillary forces, combined with the larger water storage capacity in the soil matrix, resulted in significant fracture-matrix interaction which effectively limited preferential flow down the fracture. It is also believed that fracture-matrix interaction reduced the influence of fracture roughness and other related small-scale fracture properties. The results imply that aperture variability within individual fractures may be neglected when modeling water flow through unsaturated soils. Nevertheless, fracture flow was still an important process since the fracture carried the majority of the water flow and virtually all of the mass of a surface applied tracer to depth in the soil profile. Model runs designed to assess transport variability under a variety of different physical settings, including a wider range of soil types, were also completed. Vertical contaminant fluxes were examined at several depths in the soil profile. The results showed that the presence of macropores (in the form of fractures) was more important than matrix permeability in controlling the rate of contaminant migration through soils. The depth of contaminant migration was strongly dependent on the antecedent moisture content and the presence of vertically connected fractures. Soil moisture content played a pivotal role in determining the onset and extent of preferential flow, with initially wet soils much more prone to macropore flow and deep contaminant migration. Simulations showed that surface applied tracers were able to reach the base of 2 m thick fractured soil profiles under wetter soil conditions (i.e., shallow water table). Likewise, long-duration, low-intensity rainfall events that caused the soil to wet up more resulted in proportionately more contaminant flux at depth. Fractured soils were particularly susceptible to rapid colloid movement with particle travel times to depths of 2 m on the order of minutes. The main implication is that the vulnerability of shallow groundwater is related more to vertical macropore continuity and moisture conditions in the soil profile, rather than traditional factors such as soil thickness and permeability. Macropore flow and transport processes under field conditions were investigated using small-scale infiltration experiments at sites in Elora and Walkerton, Ontario. A series of equal-volume infiltration experiments were conducted at both sites using a tension infiltrometer (TI) to control the (negative) infiltration pressures and hence the potential for macropore flow. A simulated rainfall experiment was also conducted on a small plot at Walkerton for comparison with the TI tests. Brilliant Blue FCF dye and fluorescent microsphere tracers were applied in all tests as surrogates for dissolved and colloidal contaminant species, respectively. Upon completion of infiltration, excavations were completed to examine and photograph the dye-stained flow patterns, map soil and macropore features, and collect soil samples for analysis of microspheres. Cylindrical macropores, in the form of earthworm burrows, were the most prevalent macropore type at both sites. In the TI tests, there was a clear relationship between the vertical extent of infiltration and the maximum pressure head applied to the TI disc. Larger infiltration pressures resulted in increased infiltration rates, more spatial and temporal variability in soil water content, and increased depths of dye penetration, all of which were attributed to preferential flow along macropores. Preferential flow was limited to tests with applied pressure heads greater than -3 cm. Under the largest applied pressures (greater than -1.0 cm), dye staining was observed between 0.7 and 1.0 m depth, which is near the seasonal maximum water table depth at both field sites. The tension infiltrometer was also used to infiltrate dye along an exposed vertical soil face, thereby providing a rare opportunity to directly observe transient macropore flow processes. The resulting vertical flow velocities within the macropores were on the order of tens of meters per day, illustrating the potential for rapid subsurface flow in macropores, even under partially saturated conditions. The results suggest that significant flow occurred in partially saturated macropores and this was supported by simple calculations using recent liquid configuration models for describing flow in idealized macropores. On all excavated sections, microspheres were preferentially retained (relative to the dye) in the top five centimeters of the soil profile. Below this zone, dye patterns correlated well with the presence of microspheres in the soil samples. There was evidence for increased retention of microspheres at lower water contents as well as a slightly greater extent of transport for smaller microspheres. In general, the microsphere and dye distributions were clearly dictated by vadose zone flow processes. As in the numerical experiments, water storage in the soil matrix and related macropore-matrix interaction were important factors. Mass transfer of water through the macropore walls promoted flow initiation in the macropores near surface. Deeper in the soil, water drawn away from the macropores into the matrix significantly retarded the downward movement of water along the macropores. Imbibition of dye from the macropores into the matrix was repeatedly observed on excavated soil sections and during the transient dye test. Microspheres were also transported laterally into the soil matrix indicating that conceptual models for colloid transport in the vadose zone need to account for this mass transfer process. Overall, the tension infiltrometer performed extremely well as a tool for controlling macropore flow under field conditions and, together with the dye and microsphere tracers, provided unique and valuable insights into small-scale flow and transport behavior. The field experiments raise concerns about the vulnerability of shallow groundwater in regions with thin, macroporous soils. Only a fraction of the visible macropores contributed to flow and transport at depths greater than 40 cm. However, with dye and microsphere transport observed to more than 1.0 m depth, rapid macropore flow velocities, and the sheer number of macropores present, there was clearly potential for significant flow and transport to depth via macropores. Under the right conditions, it is reasonable to speculate that macropores may represent a significant pathway for migration of surface applied contaminants to groundwater over the course of a single rainfall event.

Moisture dynamics in the critical zone have significant implications for a variety of hydrologic processes, from water availability to plants, to infiltration and groundwater recharge rates. These processes are perturbed by events such as wildfires, which may have long-lasting impacts. In September 2011, the most destructive wildfire in Texas history occurred in and around Bastrop State Park, which was significantly affected; thus this is a rare opportunity to study soil moisture under such burned conditions. A 165 m long transect, bridging burned and unburned areas, was established within the “Lost Pines” of the park. Soil moisture was monitored using a variety of methods, including 2D electrical resistivity imaging (using dipole-dipole and Schlumberger configurations), handheld measurements using a ThetaProbe, and readings at depth using PR2 profile probes. Field measurements were collected at approximately one-month intervals to study temporal and seasonal effects on soil moisture. Greater soil moisture was found near the ground surface at the heavily burned end of the transect, where the majority of trees were killed by the fire and grasses now dominate, and lower near-surface soil moisture and higher resistivity at the opposite end of the transect, which is still populated by pine trees. These variations can likely be attributed to the vegetative variations between the two ends of the transect, with trees consuming more water at one end and the ground cover of grasses and mosses consuming less water and helping reduce evaporation at the burned end. Soil texture differences could also be a factor in greater soil moisture retention at the burned end of the transect. Given the higher moisture throughout the soil profile at the burned end of the transect, this could be an indication of greater infiltration, and could increase recharge, at least in the short term. / text