Closed surface depressions, also known as “potholes” play an important role in the hydrologic cycle and provide multiple environmental services including flood mitigation, water quality improvements and wildlife habitat. In the Prairie Pothole Region, which covers approximately 715,000 km2, including parts of three Canadian provinces (Saskatchewan, Manitoba, and Alberta) and five states in the U.S. (Minnesota, Iowa, North and South Dakota, and Montana), these potholes are typically farmed and are a dominant feature in the landscape. In this study, we evaluate the Annualized Agriculture Non-Point Source (AnnAGNPS) model for simulating the inundation behavior of two farmed potholes, termed Bunny and Walnut, in Prairie Pothole Region (PPR) of Iowa. Performance analysis considered the entire growing season (GS), corresponding to the span in which there was observed data, and only days in which water storage (WS) was observed. Results show that AnnAGNPS predicted pothole water depth acceptably but not pothole water volume because of the model’s inability to accurately represent the depth-volume relationship of a pothole. When calibrated to depth, Nash-Sutcliffe efficiency (NSE) values were 0.77 and 0.24 in the Walnut pothole and 0.56 and 0.30 in the Bunny pothole, for the GS calibration and validation periods, respectively. Our results demonstrate that the AnnAGNPS model can be used to predict the inundation depth of drained and farmed potholes, which is useful for assessing landscape impacts of these features. Appropriate applications of this model could include impact of inundation on crop yield or simulations of alternative farm management strategies to compare water delivery to the potholes.