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Currently, artisanal fisheries in fresh water reservoirs have been losing ground to commercial fish farming and a great deal of fishery resources are being threatened by human interventions, such as reservoir management and increasing net-cage aquaculture. This study aims to understand the impacts of environmental changes on fishery resources and analyse the migratory fish breeding season as a missing link for fishery management in the semi-arid area of the Sao Francisco River Basin. Among the 870 fishermen operating in the Pernambuco part of the Itaparica Reservoir, 10% were interviewed and affirmed that fish stocks have been compromised due to the closed fishing period’s incoherence, exotic species insertion, and changes to the river flow caused by reservoir construction and operation. A significant correlation was observed between the Reproductive Activity Index (RAI) and precipitation (p = 0.745) as well as between the RAI and the river’s flow (p = -0.909). This shows how important it is to consider both the semi-arid climate setting and reservoir operation in determining the closed period which should safeguard fish reproduction. Monitoring the fish reproduction period and research on the reproductive biology of native fish species is needed in the Sao Francisco River Basin’s different stretches in order to guarantee valuable fish stocks and fisheries maintenance. Integrated action between the fish resource users, civil society, and federal bodies/agencies is essential in order to mitigate impacts and improve fish production systems, not only in Brazil, but in other regions experiencing a similar scenario.