Bojonegara District, having a strategic location in the coastal area of Banten Bay, is undergoing rapid industrial development. The economic activities in coastal areas simultaneously increase the ecological pressure on ecosystems and coastal resources. Ecosystem stress, directly and indirectly, disrupts organisms' life on land and in waters, causing physical, chemical, and biological changes in coastal areas of Bojonegoro District to Lima Island, causing a potential impact on socio-anthropogenic activities. This research uses a mixed qualitative and quantitative approach through observational data and literature review to estimate the economic loss that occurs if one element in the coastal area is disturbed, impacting the whole system. The water sample was collected at fifteen spots, including industrial, port, and monitoring stations along the coastal areas of Bojonegoro District to Lima Island, to assess the severity of the impacts of industrial pollution. Total economic loss is calculated using the productivity and replacement cost approach to analyze the loss value of damage on three seagrass ecosystem functions. The total loss value due to damage is estimated to be more than IDR. 950 million per year. This study finds the high economic loss is due to the low level of public knowledge and awareness, as only ≤19% of the research respondents recognize the types of ecosystem variations in coastal areas, their existence, current conditions, and utilization. This study also finds that the industry still commits environmental violations in various cases, which the stakeholders must resolve to avoid further environmental damage.