The spatiotemporal variations in hydrography and trophic status were investigated in an anthropogenically challenged tropical coastal embayment (Kakinada Bay) on the east coast of India. Water quality sampling was conducted from April 2016 to March 2017, and information on different physicochemical and biological parameters was gathered. Data sets suggested strong salinity gradients from south to north with significant seasonal fluctuations, ranging from 32.46 to 33.14 during the pre-monsoon, 19.31 to 31.59 in the monsoon, 20.53 to 24.98 in the post-monsoon, and 28.12 to 31.49 during the recovery period. Through multivariate analysis of water quality data, it was observed that the hydrographical characteristics of the south Bay differed from those of the north Bay during the pre-monsoon and recovery periods. In the monsoon and post-monsoon seasons, the salinity-nutrient gradients were influenced by river influx through the mangroves in the south and sea incursion through the Bay mouth in the north. Notably, elevated nutrient levels in the north Bay during the pre-monsoon and recovery periods indicated that urban and industrial discharges were significant pollution sources when the monsoonal influx was minimal. Assessing the trophic status of Kakinada Bay waters using Trophic State Index (TRIX) analysis revealed considerable spatial and seasonal variability. The north Bay, influenced by neritic conditions and monsoonal flushing across different seasons, consistently displayed lower TRIX values than the south Bay. Seasonally, TRIX values ranged from 2.19 to 7.56 (average: 5.4) in the pre-monsoon, 1.38 to 7.60 (average: 5.49) in the monsoon, 2.53 to 7.71 (average: 5.93) in the post-monsoon, and 2.37 to 7.93 (average: 5.16) in the recovery period. Most TRIX values (84% of total data points) categorized Kakinada Bay as a mesotrophic to eutrophic environment. These findings align with our previous study on macrobenthos and bottom sediment characteristics, indicating that continuous anthropogenic interventions have significantly degraded the water quality of the Bay. Consequently, the Bay environment is poised to become an environmentally and ecologically costly concern in the near future. To mitigate these issues, the government should implement measures to reduce urban discharges and increase flushing rates within the Bay.