Coastal aquaculture zones, including areas for shrimp and mollusk farming, are subject to multiple stressors, such as internal farming activities, inland runoff, and extreme weather events driven by climate change. These factors contribute to spatiotemporal fluctuations in water quality, directly affecting aquaculture productivity and sustainability. This study aims to assess the current status of water quality in shrimp and clam farming areas across coastal districts of Nam Dinh Province, Vietnam, identify spatial and temporal variation trends, and propose appropriate management measures. Environmental parameters, including pH, dissolved oxygen (DO), salinity, alkalinity, COD, ammonium (N-NH₄⁺), nitrite (N-NO₂⁻), hydrogen sulfide (H₂S), total suspended solids (TSS), and total vibrio count, were monitored biweekly. The results indicated significant temporal fluctuations in water quality, with a clear deterioration trend during the rainy season and in storm-affected months, particularly in September, during the passage of Typhoon Yagi. In shrimp farming areas, water source quality tended to decline during June–August. Localized differences were also observed: Nghia Hung was characterized by low DO levels, while Hai Hau experienced large salinity fluctuations. In clam farming zones, water quality was lowest in June and July. Giao Thuy exhibited a higher frequency of salinity values falling below acceptable thresholds compared to Nghia Hung, suggesting greater variability in salinity levels. These findings provide a scientific basis for local authorities and farmers to plan adaptive water management strategies, such as storing high-quality water for use during periods of environmental stress.