Large flow-through reservoirs and lakes possess environmental gradients and monitoring programs are mostly adapted for cost and time effectiveness. Bay areas are often more isolated from the main water body and are likely to have unobserved different environmental processes and impacts. This study was performed at the Itaparica Reservoir, São Francisco River, located in semi-arid Northeast Brazil, with dendritic form. Water residence time in the Icó-Mandantes Bay was estimated by hydrodynamic flow and transport simulations. The P-chlorophyll a relationship was used to develop the P use efficiency coefficient for critical P load estimation of 25 μg P L-1. Phosphorus sources and input rates into a bay and the respective reservoir were calculated and compared regarding their different origins for the period after flooding (1988) and for 2013. After impoundment, the P load highly exceeded the carrying capacity because of leaching and mineralization processes. In 2013, P inputs were still above this threshold, whereas inflow and sub-basin P export during the rainy season were crucial. But eutrophication processes have increased in the bay relative to the main water body. Hence, water in hydraulic isolated parts is prone to eutrophication processes, thus, bays have to be specially considered in water resource management.