Environmental monitoring is essential to assess and, if possible, anticipate the consequences of various marine economic developments. This study describes progress in environmental monitoring by developing and applying a eutrophication index (EI) for marine protected areas (MPAs). The EI combines available data, such as biological oxygen demands, dissolved inorganic nitrogen and phosphorus, and chlorophyll-a, with the weighting factors calculated from principal component analysis to assess environmental quality. Its effectiveness was tested using nearly three decades of environmental data (since 1996) from the Nha Trang MPA in Vietnam. The EI revealed clear trends in environmental quality. In the period 1996–2006, environmental conditions deteriorated, negatively impacting aquaculture. In the later period, 2007–2024, improved environmental protection policies, technological developments, expanding tourism, and heightened public awareness contributed to a reversal of this trend. During the earlier period, the EI indicated poor environmental quality (Level V), while in the later years, it improved significantly, approaching Level II. This study also identified the spatial eutrophication patterns and helped to determine the causes of specific eutrophication levels. These included port development, aquaculture activities, and domestic waste discharge. These findings highlight the close relationship between environmental quality and economic activities in the bay. Overall, the new EI and its sensitivity maps enhance environmental monitoring capabilities. They provide valuable tools for decision-makers, aiding in the strategic planning of marine economic development, ecosystem protection, and sustainable resource use. The approach supports long-term environmental stewardship and more informed, adaptive management of coastal and marine areas.