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Reservoir bays, at the terrestrial and water boundary, where water fluidity slows down and self-purification ability turns weak, hence they are especially sensitive to terrestrial exogenous pollutants, even resulting in eutrophication. According to N:P, water nutrient types can be divided into N limited, P limited and N + P limited classes. Phytoplankton biomass is represented by chlorophyll a, which is one of the sensitive indicators of water eutrophication. Comprehensively tracing non-point pollution from terrestrial exogenous pollutants (fertilizer, soil release, anthropogenic discharge) to water nutrients that happen in reservoir bays is of great significance. This paper identified the dominant environmental variables and nutrients' limited types of reservoir bays at storage and discharge periods, and constructed a partial least squares structural equation model (PLS-SEM) to explore the impacts of terrestrial exogenous pollutants. Results showed that in the storage period, water contamination mainly came from residential discharge and soil endogenous release, and the total contribution rate reached 61%. In the discharge period, with the increase of rainfall–runoff erosion, the explanatory ability of land use, topography and landscape pattern to water quality increased, up to 58%. The dominant nutrient limited types of reservoir bays were P limited (35%–47%) and N + P limited (35%–59%) at both stages, N limited situations were less than 20% and generally appeared in the storage period. Whatever the nutrient limited type was, phosphorus always had a higher effect on phytoplankton biomass. In the N limited situation, nitrogen came mainly from soil release (total effect = 0.6) and phosphorus from fertilizer (total effect = 0.22) and soil release (total effect = 0.17). In the P limited situation, all three sources had almost high effects on nitrogen, phosphorus, and phytoplankton biomass. In the N + P limited situation, anthropogenic discharge was the main source of nutrients and the primary threat factor for phytoplankton biomass. The approaches employed in this study could be generalized to other basins and the results were significant for early warning and controlling water eutrophication. HIGHLIGHTS The relationships between the terrestrial exogenous input with the nutrient limited types were explored.; The dominant nutrient limited types of reservoir bays were P limited and N + P limited at both stages.; Whatever the nutrients limited type was, phosphorus always had higher effect on phytoplankton biomass.; The effects and contributions of fertilizer, soil release and anthropogenic discharge to water nutrients and phytoplankton biomass were calculated.;