In the Chattahoochee River downstream of Lake Sidney Lanier Dam, there is significant fish hatchery operation managed by the Georgia Department of Natural Resources (GA-DNR) and the Georgia Fish and Wildlife Department. Recently, fish hatcheries have reported unexplained mortality events among hatchlings, raising concerns about environmental influences on fish production. QSWAT watershed hydrologic model was developed through efficient Scripting and USGS API Modifications to determine the changes in daily nutrient loading to the hatchery locations. Results revealed that spikes in ammonia (NH₄) concentration—primarily linked to poultry litter prevalent in the watershed—were associated with sudden drops in water temperature, likely contributing to hatchling mortality. These findings underscore the influence of watershed land use and nutrient loading on aquatic habitat conditions and fish survival. The study provides a data-driven foundation for decision support in managing fish hatcheries under changing watershed and climate conditions.