Considering the environmental impacts to rivers caused by the exploitation of water resources and the consequences of these impacts upon fauna, the objective of this study was to evaluate the population biology of the shrimp Atya scabra (Leach, 1816) in the final stretch of the major river of South America. This species was assessed as “Near Threatened” in the red book of Brazilian crustaceans. Specimens were sampled monthly from February 2015 to January 2016 in a region of the lower São Francisco River, Brazil. A total of 233 individuals of A. scabra were collected, including 120 males and 113 females (71 non-ovigerous and 42 ovigerous). Atya scabra abundance was higher when water flow values increased. A decrease in abundance was observed over the one year of sampling, indicating a decline of about 90 % in this population in this region of the São Francisco River. We suggest that this decline was caused by the reduction of water flow in the São Francisco River, due to a policy that authorized retaining more water behind dams and releasing less water into the river in April and June 2015. In light of this, other studies should monitor the population dynamics of this species, while legislative actions are also needed to protect this fragile ecosystem.