Industrial activities in coastal areas can produce pollutant substances that are detrimental to the ecological environment. This study aimed to assess the ecological risks of heavy metal pollution in water, sediments, and polychaeta (Neoleanira tetragona) affected by aquaculture, urban rivers, and ports. Water parameters such as temperature, DO, pH, and salinity were measured in situ at fifteen observation stations. Samples were taken at three locations around the aquaculture area, namely the Barong River, the Musi River Estuary as an urban river area, and Tanjung Api-api port in South Sumatra, Indonesia. Analysis of sediment grain size and substrate types using the method of Shepard's triangle Heavy metal concentrations were measured by graphite furnace atomic absorption spectrometry. Then, the data were analyzed using one-way analysis of variance (ANOVA) and post-hoc Tukey statistical analysis. Ecological risk assessment uses the Bioconcentration Factor (BCF), Index Geoaccumulation (Igeo), Contamination Factor (Cf), and Pollution Load Index (PLI). Based on the results, the concentration of heavy metal Pb in water was not detected until 0.625 mg/L, and Cu was not detected. Furthermore, Pb in sediments was 1.261–11.070 mg/kg, Cu was 0.193–19.300 mg/kg, Pb polychaeta was not detected until 0.0044 mg/kg, and Cu ranged from 0.0003–0.0014 mg/kg. Ecological risk assessment for BCF showed that the level of accumulation of polychaeta (N. tetragona) was categorized as an excluder (BCF < 1). Igeo and Cf indicate uncontaminated pollution levels (Igeo < 0) and low contamination (Cf < 1). Meanwhile, the Pollution Load Index is included in the non-polluted category (PLI <0). Based on the results, the quality of the ecological environment affected by aquaculture, urban rivers, and ports is still classified as safe for ecological risk assessment; further studies are needed regarding the relationship between pollution levels and the physiological response of biota.