Mariculture is a key protein source and economic driver but traditional methods pollute coastal waters, hindering sustainable development. Current research on the ecological impacts of mariculture mainly focuses on specific pollutants and lacks an assessment of the biogeochemical impacts of mariculture discharge. This study examined Xiangshan Bay, a representative intensive mariculture area in China, to explore the impact of mariculture tailwater discharge on water quality, focusing on dissolved organic matter (DOM) and bacterial communities. Based on the fluorescence excitation-emission matrix combined with parallel factor analysis, a characteristic fluorescence component C4 was identified in mariculture tailwater (intensity of 40 ± 4 %, n = 8), while higher C4 components (47 ± 3 %, n = 15) were found throughout the bay. Humic-like components from riverine input (C1 + C2: 32 ± 3 %, n = 15) and protein-like components from domestic sewage (C5: 2 ± 1 %, n = 15) were significantly lower in the seawater samples, indicating the strong influence of mariculture tailwater on the entire DOM structure of the bay. The bacterial community structure showed a response consistent with DOM, as revealed by nonmetric multidimensional scaling analysis. This showed that bacterial communities in mariculture tailwater and bay water samples clustered together, independent of riverine input. The SourceTracker model indicated that mariculture tailwater (91 ± 5 %) predominantly contributed to the bacterial community, with minimal contributions from riverine input (< 5 %). Co-occurrence network analysis further showed that under long-term high-intensity mariculture discharge, the C4 component became the core DOM and was closely associated with the bacterial community. The results here demonstrate the profound impact of traditional mariculture on coastal water quality and show that riverine input is not the primary pollution source in this region, providing clear directions for coastal environmental restoration efforts.