Since most wetlands in the Sacramento Valley of California are dependent on artificial water delivery, supplying water for wetland management is the greatest challenge to wetland managers, especially during drought years. Efforts are needed to improve the security of water supplies for optimal habitat management and water quality improvement. This study contributes to these efforts by developing an eco-hydrologic model (Agricultural Policy/ Environmental Extender [APEX]) of this wetland system, which has key components evaluated in the wetland simulation, including wetting and drying of wetland soils, competition and response of wetland species to wetland hydrology, settling of sediment, and nitrogen (N) removal. APEX model calibration (April of 2017 to May of 2018) and validation (June of 2018 to August of 2018) resulted in a percentage bias (PB) of 9.8% and-8.5%, respectively, for total volume of water holding in four serially connected wetlands. The N contents in the wetland waterbody were calibrated and validated using the monitored values collected during 2017 to 2018 and 2015 to 2016, respectively. All PB values for calibration and validation were over 35%. The calibrated model was used to evaluate the effects of wetland management and increasing temperature on N removal. Moreover, an additive regression model (ARM) was developed based on bird survey data and used to analyze bird dropping seasonal patterns and access their impacts on water quality in the studied wetlands. Based on the results of the model, the wetland water quality was influenced by waterfowl populations and eventually governed by water availability in each wetland cell. The N removal by wetlands was negatively affected by the volume of irrigation water. Moreover, increasing temperature caused a decrease in waterfowl population, which led to decreased N concentration by up to 42%. Overall, the results indicate that the developed model can be effectively used to quantify the effects of wetland management on water balance, water quality, and vegetation and to describe the nexus of wetland management, water use, and ecosystem service functions of managed wetlands.