We investigated the diversity of testate amoebae in an urban stream located within the Igarapé São Francisco Environmental Protection Area in Acre, northern Brazil, during the dry season, and evaluated the factors mediating the structure of this protist community. We collected 108 water samples for the analysis of the testate amoeba community and the limnological variables at six sampling points on the stream, between July and September 2018. We used a Redundancy Analysis (RDA) to verify the influence of environmental variables on the protist community. We recorded 76 species of testate amoebae from eight families, with most records from the families Difflugiidae, Arcellidae, Centropydae and Netzeliidae. More than half (49) of the species were recorded in Acre for the first time. The abundance of the amoebae of the family Trigonopiridae was regulated by the dissolved oxygen concentrations and the pH, while that of the Netzeliidae, Dif-flugiidae and Lesquereusidae was influenced by the pH, chloride concentrations, and the depth and transparency of the water. In the case of the family Arcellidae, abundance was determined by the turbidity and transparency of the water and the nitrate concentrations, while that of Centropyxis sp. was associated with the concentrations of thermotolerant coliforms. These findings indicate that, while the São Francisco stream is subject to anthropogenic impacts, it still presents adequate conditions for these organisms in some of its stretches. The abundance of these amoebae was influenced primarily by the productivity of the system, as indicated by the high protist densities recorded in the areas in which primary productivity was highest. These findings support the use of these protists in studies that investigate the most appropriate indicator organisms that respond to anthropogenic impacts and shifts in environmental quality.The results of the present study demonstrated the importance of this aquatic ecosystem for the biodiversity of the study area, and the need to further expand our knowledge on the adaptations and interactions of the aquatic communities of the Amazon region.