Municipal wastewater discharge into the adjacent seas is the most common practice of final wastewater disposal in coastal cities worldwide. To mitigate serious water pollution, treatment of municipal wastewater has advanced rapidly in China's coastal cities since 2005. However, because of differential nutrient removal efficiencies in wastewater treatment, ratios between different nutrients in wastewater can change significantly after being treated, which imposes a bottom-up effect for the growth of phytoplankton in receiving waters. In this study, we had characterized temporal changes of TN, TP and NH₃–N discharges and their ratios in municipal wastewater in China's coastal cities during 2006–2015. Results showed that in 2015, a total of 296 Gg of TN, 37 Gg of TP, and 256 Gg of NH₃–N were discharged into nearshore waters by municipal wastewater. Much higher TP and NH₃–N removal efficiencies (82% and 92%, respectively) than TN (63%) in wastewater treatment were observed, which had increased TN/TP and TN/NH₃–N mass ratios by about twice and five times, respectively, in the effluents relative to the influents. As the percentage of municipal wastewater being treated increased, significant increases in TN/TP and TN/NH₃–N ratios in the total municipal wastewater discharge into nearshore waters had occurred. Simple correlation analysis showed that differences in nutrient ratios in municipal wastewater discharge in coastal cities might be related with the spatial variations of nutrient ratios in nearshore waters. Our results suggest that a long-term strategy for municipal wastewater management in coastal cities should not merely focus on the reduction of nutrient discharge, but also consider more balanced nutrient regimes to maintain aquatic biodiversity in nearshore waters.