Coastal ecosystems are important destinations for natural and anthropogenic inputs, areas experiencing eutrophication from untreated sewage globally. However, the mechanistic link of how coastal waters and sediments can jointly respond to nutrient enrichment, especially nitrogen (N) and phosphorus (P), remains relatively unknown. Here, we assessed the interdecadal variability in N and P contents, comparing four surface water sampling sites (∼40-year monthly concentrations) and three 210Pb dated sediment cores (∼70-years) in an urban bay that has received increasingly high untreated sewage discharges over the past century (Guanabara Bay, Brazil). Major eutrophication was found, with differences between waters and sediments along sampling sites. The water concentrations of total phosphorus (TP) and dissolved inorganic nitrogen (DIN) yielded on average ∼10–45 % and ∼40–190 % higher in 2005–2017 compared to 1980–2005 period in the sampling site most influenced by the denser urban than the conserved area, respectively. Furthermore, 6-year average water concentrations indicated both recent initial decreases in the most urban area, potentially associated with new sanitation facilities, and high increases in those relatively more conserved areas. Conversely, TP and TN sediment burial rates were less sensitive to recent changes as compared to the water concentrations, yielding ∼11 and 31 % between 1980–2005 and 2005–2017, respectively, of which also provided baselines data for earlier periods without direct pelagic measurements (i.e., 1950–1980). Thus, these findings offer new insights into substantial temporal and intra-ecosystem spatial variability of coastal eutrophication, indicating that an integrated analysis between water monitoring and sediment burial is needed to improve the diagnosis and prediction capabilities necessary for effective long-term mitigation of coastal aquatic eutrophication worldwide.