The increasing riverine pollutants have resulted in nutrient enrichment and deterioration of water quality in the coastal water of Guangxi Province, China. However, the quantitative relationship between nutrient loads and water quality responses, which is crucial for developing eutrophication control strategies, is not well studied. In this study, the riverine fluxes of nutrients were quantified and integrated with nutrient cycling and phytoplankton dynamics by using box models for Guangxi coastal bays. The model concepts and biogeochemical equations were the same; while most model parameters were specific for each bay. The parameters were calibrated with seasonal observations during 2006–2007, and validated with yearly averaged measurements in 2009. The general features of nutrient and phytoplankton dynamics were reproduced, and the models were proved feasible under a wide range of bay conditions. Dissolved inorganic nitrogen was depleted during the spring algal bloom in Zhenzhu Bay and Fangcheng Bay with relatively less nutrient inputs. Phosphorus concentration was high in spring, which decreased then due to continuous phytoplankton consumption. Chlorophyll-a concentration reached its annual maximum in summer, but was the minimum in winter. Eutrophication was characterized by both an increase in nutrient concentrations and phytoplankton biomass in Lianzhou Bay. Either about 80% reduction of nitrogen or 70% reduction of phosphorus was required to control the algal bloom in Lianzhou Bay. Defects of the models were discussed and suggestions to the environmental protection of Guangxi coastal bays were proposed. The increasing riverine pollutants have resulted in nutrient enrichment and deterioration of water quality in the coastal water of Guangxi Province, China. However, the quantitative relationship between nutrient loads and water quality responses, which is crucial for developing eutrophication control strategies, is not well studied In this study, the riverine fluxes of nutrients were quantified and integrated with nutrient cycling and phytoplankton dynamics by using box models for Guangxi coastal bays. The model concepts and biogeochemical equations were the same; while most model parameters were specific for each bay. The parameters were calibrated with seasonal observations during 2006-2007, and validated with yearly averaged measurements in 2009. The general features of nutrient and phytoplankton dynamics were reproduced, and the models were found feasible under a wide range of bay conditions. Dissolved inorganic nitrogen was depleted during the spring algal bloom in Zhenzhu Bay and Fangcheng Bay with relatively less nutrient inputs. Phosphorus concentration was high in spring, which decreased then due to continuous phytoplankton consumption. Chlorophyll-a concentration reached its annual maximum in summer, but was the minimum in winter. Eutrophication was characterized by both an increase in nutrient concentrations and phytoplankton biomass in Lianzhou Bay. Either about 80% reduction of nitrogen or 70% reduction of phosphorus was required to control the algal bloom in Lianzhou Bay. Defects of the models were discussed and suggestions to the environmental protection of Guangxi coastal bays were proposed.