Human-induced nutrient inputs to global coastal waters are leading to increasing nutrients and escalating eutrophication. However, how aquatic ecosystem functioning responds to these changes remains insufficiently studied. Here we report the long-term changes in the nutrient regime and planktonic ecosystem functioning in the Daya Bay, a typical subtropical semi-enclosed bay experiencing rapid economic and social development for several decades. Time-series (from 1991 to 2018) data with a mostly quarterly resolution were collected to depict long-term changes in dissolved inorganic nutrients and plankton abundances, based on which we constructed simplified abundance size spectra (SASS) and plankton abundance ratios to describe the functioning of the planktonic ecosystem. The results revealed a long-term increase in system productivity but a decrease in integrated energy transfer efficiency of the planktonic ecosystem, with rising concentrations of dissolved inorganic nitrogen (DIN). Shifts in the nutrient regime and planktonic ecosystem functioning were detected at a tipping point or threshold around 2006–2007. The shifts were characterized by abrupt changes in the trends of nutrient (phosphate, ammonia, nitrite) concentrations, nutrient ratios (DIN/phosphate, silicate/phosphate), plankton abundance, and total plankton biomass. Compared to the nutrient regime, the planktonic ecosystem functioning shifted several years later. Overall, this study indicates that the pelagic ecosystem regime can shift significantly in response to long-term increasing input of human-induced nutrients in coastal waters such as the Daya Bay. The regime shifts may have profound implications for fishery production, and ecosystem management in the bay.