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Quantifying the magnitude and timing of groundwater returns to streams from irrigation is important for the management of natural resources in irrigation districts where the quantity or quality of surface water can be affected. Deep vadose zones and perched water tables can complicate the modelling of these fluxes, and model outputs may be biased if these factors are misrepresented or ignored. This study was undertaken in the Murray Basin in southern Australia to develop and test an integrated modelling method that links irrigation activity to surface water impacts by accounting for all key hydrological processes, including perching and vadose zone transmission. The method incorporates an agronomic water balance to simulate root zone processes, semi-analytical transfer functions to simulate the deeper vadose zone, and an existing numerical groundwater model to simulate irrigation returns to the Murray River and inform the management of river salinity. The integrated modelling can be calibrated by various means, depending on context, and has been shown to be beneficial for management purposes without introducing an unnecessary level of complexity to traditional modelling workflows. Its applicability to other irrigation settings is discussed.

Marine ecosystems are sensitive to inputs of chemicals from submarine groundwater discharge. Tidally influenced saltwater-freshwater mixing zones in beach aquifers can host biogeochemical transformations that modify chemical loads prior to discharge. A numerical variable-density groundwater flow and reactive transport model was used to evaluate the physical controls on reactivity for mixing-dependent and mixing-independent reactions in beach aquifers, represented as denitrification and sulfate reduction, respectively. A sensitivity analysis was performed across typical values of tidal amplitude, hydraulic conductivity, terrestrial freshwater flux, beach slope, dispersivity, and DOC reactivity. For the model setup and conditions tested, the simulations demonstrate that denitrification can remove up to 100% of terrestrially derived nitrate, and sulfate reduction can transform up to 8% of seawater-derived sulfate prior to discharge. Tidally driven mixing between saltwater and freshwater promotes denitrification along the boundary of the intertidal saltwater circulation cell in pore water between 1 and 10 ppt. The denitrification zone occupies on average 49% of the mixing zone. Denitrification rates are highest on the landward side of the circulation cell and decrease along circulating flow paths. Reactivity for mixing-dependent reactions increases with the size of the mixing zone and solute supply, while mixing-independent reactivity is controlled primarily by solute supply. The results provide insights into the types of beaches most efficient in altering fluxes of chemicals prior to discharge and could be built upon to help engineer beaches to enhance reactivity. The findings have implications for management to protect coastal ecosystems and the estimation of chemical fluxes to the ocean.

Beach aquifers host a dynamic and reactive mixing zone between fresh and saline groundwater of contrasting origin and composition. Seawater, driven up the beachface by waves and tides, infiltrates into the aquifer and meets the seaward-discharging fresh groundwater, creating and maintaining a reactive intertidal circulation cell. Within the cell, land-derived nutrients delivered by fresh groundwater are transformed or attenuated. We investigated this process by collecting pore water samples from multilevel wells along a shore-perpendicular transect on a beach near Cape Henlopen, Delaware, and analyzing solute and particulate concentrations. Pore water incubation experiments were conducted to determine rates of oxygen consumption and nitrogen gas production. A numerical model was employed to support field and laboratory interpretations. Results showed that chemically sensitive parameters such as pH and ORP diverged from salinity distribution patterns, indicating biogeochemical reactivity within the circulation cell. The highest respiration rates were found in the landward freshwater-saltwater mixing zone, supported by high dissolved inorganic carbon. Chlorophyll a, a proxy for phytoplankton, and particulate carbon did not co-occur with the highest respiration rates but were heterogeneously distributed in deeper and hypoxic areas of the cell. The highest rates of N2 production were also found in the mixing zone coinciding with elevated O2 consumption rates but closer to the lower discharge point. Model results were consistent with these observations, showing heightened denitrification in the mixing zone. The results of this work emphasize the relationship between the physical flow processes of the circulation cell and its biogeochemical reactivity and highlight the environmental significance of sandy beaches.

Publisher version available following 6 months embargo from date of publication (9 November 2016) in accordance with publisher copyright requirements., The occurrence of freshwater lenses in saline aquifers adjoining gaining rivers has recently been demonstrated as being theoretically possible by way of analytical solution. However, physical evidence for freshwater lenses near gaining rivers is limited largely to airborne geophysical surveys. This paper presents the first direct observations of freshwater lenses adjacent to gaining rivers, albeit at the laboratory-scale, as validation of their plausibility. The experimental conditions are consistent with the available analytical solution, which is compared with laboratory observations of lens extent and the saltwater flow rate, for various hydraulic gradients. Numerical simulation shows that dispersion can account for the small amount of mismatch between the sharp-interface analytical solution and laboratory measurements. Calibration and uncertainty analysis demonstrate that accurate mathematical predictions require calibration to laboratory measurements of the lens. The results provide unequivocal proof that freshwater lenses can persist despite gaining river conditions concordant with theoretical lenses predicted by the analytical solution, at least within the constraints of the experimental setup.

Published version made available following 6 months embargo from date of publication (13 May 2016) in accordance with publisher copyright., Rivers in arid and semiarid regions often traverse saline aquifers, creating buoyant freshwater lenses in the adjoining riparian and floodplain zones. The occurrence of freshwater lenses where the river is otherwise gaining saline groundwater appears counterintuitive, given that both hydraulic and density forces act toward the river. In this paper, an analytical solution is presented that defines the extent of a stable, sharp-interface terrestrial freshwater lens (in cross section) in a riverine environment that otherwise contains saline groundwater moving toward the river. The method is analogous to the situation of an island freshwater lens, except in the riverine setting, the saltwater is mobile and the lens is assumed to be stagnant. The solution characterizes the primary controlling factors of riverine freshwater lenses, which are larger for situations involving lower hydraulic conductivities and rates of saltwater discharge to the river. Deeper aquifers, more transmissive riverbeds, and larger freshwater-saltwater density differences produce more extensive lenses. The analytical solution predicts the parameter combinations that preclude the occurrence of freshwater lenses. The utility of the solution as a screening method to predict the occurrence of terrestrial freshwater lenses is demonstrated by application to parameter ranges typical of the South Australian portion of the River Murray, where freshwater lenses occur in only a portion of the neighboring floodplains. Despite assumptions of equilibrium conditions and a sharp freshwater-saltwater interface, the solution for predicting the occurrence of riverine freshwater lenses presented in this study has immediate relevance to the management of floodplains in which freshwater lenses are integral to biophysical conditions.

© 2017 Elsevier. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 24 month embargo from date of publication (August 2017) in accordance with the publisher’s archiving policy, Freshwater lenses are lenticular bodies of fresh (TDS

Spatially periodic solute boundaries force symmetry across a model domain by ensuring that concentrations and concentration gradients are identical at the same location on opposite boundaries. They have been used in multiple publications on a hyporheic zone model of a single ripple or dune style bed form, including variable density flow and reactive transport variants. We evaluate simulations of multibed form models without imposing spatially periodic transport to demonstrate that nonphysical solute distributions arise from the periodic solute transport assumption. That is, the flow field within the single bed form model leads to a transport scenario that violates the forced symmetry of periodic solute boundary conditions, culminating in a physically unrealistic solute distribution. Our results show that lack of symmetry between boundaries is a function of the vertical concentration gradient and two-dimensionless parameters characterizing the hyporheic and underflow flow regimes, and the solute exchange between them. We assess the error associated with the spatially periodic assumption based on an analysis of solute fluxes across the lateral bed form model boundaries. While the focus is on steady state concentration distributions, the implications for transient solute transport models are also discussed. We conclude that periodic solute transport boundary conditions should be applied only to bed form models that have minimal vertical dispersive and diffusive solute transfer. This includes gaining systems and tracers such as temperature, for which a temporally periodic flux reversal occurs across the top boundary.

Small-scale hyporheic zone (HZ) models often use a spatial periodic boundary (SPB) pair to simulate an infinite repetition of bedforms. SPB's are common features of commercially available multiphysics modeling packages. MODFLOW's lack of this boundary type has precluded it from being effectively utilized in this area of HZ research. We present a method to implement the SPB in MODFLOW by development of the appropriate block-centered finite-difference expressions. The implementation is analogous to MODFLOW's general head boundary package. The difference is that the terms on the right hand side of the solution equations must be updated with each iteration. Consequently, models that implement the SPB converge best with solvers that perform both inner and outer iterations. The correct functioning of the SPB condition in MODFLOW is verified by two examples. This boundary condition allows users to build HZ-bedform models in MODFLOW, facilitating further research using related codes such as MT3DMS and PHT3D.

The assumption of spatial repetition is commonly made when producing bedform scale models of the hyporheic zone. Two popular solute transport codes, MT3DMS and PHT3D, do not currently provide the necessary boundary condition required to simulate spatial periodicity in hyporheic zone transport problems. In this study, we develop a spatially periodic boundary (SPB) for solutes that is compatible with a SPB that was previously developed for MODFLOW to simulate the flow component of spatially periodic problems. The approach is ideal for simulating groundwater flow and transport patterns under repeating surface features, such as ripples or dunes on the bottom of a lake or stream. The appropriate block-centered finite-difference approach to implement the boundary is presented and the necessary source code modifications are discussed. The performance of the solute SPB, operating in conjunction with the groundwater flow SPB, is explored through comparison of a multi-bedform hyporheic-zone model with a single bedform variant. The new boundary conditions perform well in situations where both dispersive effects and lateral seepage flux in the underflow regime beneath the hyporheic zone are minimal.

The freshwater resources of coastal aquifers are vulnerable to seawater intrusion (SWI) caused by the current rising trends in sea levels, amongst other factors. Recent studies have examined the extents, rates and timescales associated with SWI induced by expected levels of sea-level rise (SLR), but have neglected the effects of transgression (i.e. inland migration of the shoreline in response to SLR). In this chapter, variable-density numerical modelling is used to examine the implications of transgression for a range of SWI scenarios based on simplified coastal aquifer settings. Vertical intrusion during transgressions can involve density-driven convective processes, causing substantially larger amounts of seawater to enter the aquifer and creating more extensive intrusion than that of horizontal SWI occurring in the absence of transgression. Interestingly, cases of transgression where no vertical mixing occurs involve reduced landward migration of the wedge toe, relative to otherwise similar situations without transgression. The rates and extents of SWI caused by transgression and associated vertical mixing appear to be almost non-responsive to the choice of landward boundary condition, contradictory to the findings of SLR-SWI studies that neglect transgression. The findings of this study suggest that modelling analyses that neglect the effects of transgression in SLR-SWI investigations may underestimate significantly the rates and extent of SWI.

Small-scale hyporheic zone (HZ) models often use a spatial periodic boundary (SPB) pair to simulate an infinite repetition of bedforms. SPB's are common features of commercially available multiphysics modeling packages. MODFLOW's lack of this boundary type has precluded it from being effectively utilized in this area of HZ research. We present a method to implement the SPB in MODFLOW by development of the appropriate block-centered finite-difference expressions. The implementation is analogous to MODFLOW's general head boundary package. The difference is that the terms on the right hand side of the solution equations must be updated with each iteration. Consequently, models that implement the SPB converge best with solvers that perform both inner and outer iterations. The correct functioning of the SPB condition in MODFLOW is verified by two examples. This boundary condition allows users to build HZ-bedform models in MODFLOW, facilitating further research using related codes such as MT3DMS and PHT3D.