<p>The development of industry has promoted the economic growth, but the centralized development of industrial agglomeration has caused certain problems to the environment. In this study, a typical coastal economic development zone in eastern China is taken as the research area, and bimonthly water sampling was conducted at 48 locations within the Xichao River Basin from January to August 2022, with supplemental sediment samples collected at 9 monitoring sites in July 2022. The aquatic environment and ecosystem of the study area were investigated using an integrated approach combining field sampling, numerical modeling, and high-throughput sequencing techniques. The results show that the water quality in the park exceeds the standard seriously in the case of insufficient sewage treatment capacity, the exceedance rates of COD_Cr, BOD, petroleum pollutant, TN and As are all over 70% and the pollution degree tends to be heavier the closer to the estuary. The Canonical Correlation Analysis (CCA) method indicates that the first two axes together account for 59.76% of the community variation. Fluoride, a major pollutants from the photovoltaic industry, was identified as the key environmental factor driving microbial community changes. Ecosystem stability decreased with increasing pollution levels. Simulations using a one-dimensional water quality model confirmed that both proposed wastewater treatment plants (60,000 and 120,000 t/d capacity) would meet effluent standards. This study provides foundational research methodologies for water environmental management coastal economic development zones and offers practical insights for coastal ecosystem conservation and restoration.</p>