Estuarine environments naturally exhibit temporal and spatial variability due to the dynamic interplay of tides and freshwater discharge. These physical forces interact with resident biota and aquaculture activities, including farming and processing industries. Therefore, a comprehensive study of estuaries must account for multiple factors. To mitigate anthropogenic impacts on estuaries, it is essential to evaluate their trophic state and describe nutrient loads and eutrophication relationships. This study investigated the intensive aquaculture farming and discharge water quality in the Upputeru estuary, highlighting the region’s typical seasonality. Water quality parameters, particularly ammonia and nitrates, indicate that the Upputeru estuary is inherently prone to eutrophication due to its hydrologic characteristics and the diffuse sources from extensive shrimp farming. Moreover, chlorophyll-a levels peak in these areas, with shrimp culture effluents significantly promoting the spread of chlorophyll-a-rich waters toward the estuarine mouth. This condition is attributed to the discharge of nutrient-rich shrimp pond wastewater, which degrades water quality and boosts phytoplankton biomass in the Upputeru estuary.