Agricultural and Biological Systems Engineering, Department of
Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research
First Advisor
Aaron R. Mittelstet
Second Advisor
Troy E. Gilmore
Committee Members
Erin M.K. Haacker
Date of this Version
12-2025
Document Type
Thesis
Citation
A thesis presented to the faculty of the Graduate College at the University of Nebraska in partial fulfillment of requirements for the degree of Master of Science
Major: Agricultural and Biological Systems Engineering
Under the supervision of Professors Aaron R. Mittelstet and Troy E. Gilmore
Lincoln, Nebraska, December 2025
Abstract
Excessive application of inorganic nitrogen fertilizers has led to pervasive nitrate contamination of groundwater in agricultural regions worldwide. This study evaluates the fate and transport of nitrate beneath the Bazile Creek watershed in northeastern Nebraska by coupling groundwater‐flow (GWF) and solute‐transport (GWT) simulations within MODFLOW 6. A conceptual model was developed using hydrogeologic, topographic, recharge, and boundary‐condition data, and the domain was discretized with a quadtree-refined grid to capture surface-subsurface interactions. The steady-state flow model was calibrated against observed hydraulic heads and baseflow measurements using NSE, RMSE, and PBIAS metrics, and subsequently extended to a transient flow simulation spanning 2002-2023. The nitrate‐transport model incorporated ordinary Kriging-derived initial concentration surfaces and land‐use-based input zones and was calibrated across three temporal periods (2002-2008, 2009-2016, 2017-2023) by adjusting dispersivity, porosity, and input concentrations. Following calibration, five 100-year management scenarios were simulated: continued high agricultural nitrogen input in irrigated corn and soybean (baseline), conversion of irrigated cropland to non-irrigated cropland, conversion of cropland to rangeland, changing one-time fertilizer application to three-time application, and optimum nitrogen fertilizer application to assess long-term nitrate dynamics under alternative land-use practices. Scenario analysis revealed that agricultural management practice conversion scenarios attenuate nitrate concentrations relative to the continued high nitrogen loading baseline with continuity of present agricultural management practices. This effect was most evident in domestic wells, where nitrate concentration trends continued to rise under the baseline scenario, underscoring the value of targeted agricultural management for protecting rural water supplies. In particular, removing deep irrigation wells was not an optimal mitigation strategy in this basin: turning off irrigation reduced pumping‐related drawdown and thereby increased nitrate delivery to domestic wells and to streams via baseflow. Conversely, maintaining irrigation while implementing best management practices (BMPs), including efficient, split, and right-rate applications, most effectively reduced groundwater nitrate concentrations and simultaneously lowered baseflow NO₃-N loads, thereby balancing drinking-water protection with stream health. These results provide a robust, quantitative framework for guiding nitrate mitigation strategies in groundwater-dependent agricultural watersheds.
Advisors: Aaron R. Mittelstet and Troy E. Gilmore
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