Adult females of most black flies species (Diptera, Simuliidae) exhibit a blood-sucking habit. Immature stages develop in water courses and are important in the ecology of lotic environments. We aim to understand the distribution of immature simuliids in the hydrographic sub-basin of the Comandaí river, in Northwest of Rio Grande do Sul, Brazil. For that purpose, simuliids were sampled in three stretches (source, intermediate and mouth) of nine streams, distributed along the three main regions of the sub-basin. Evaluations of the influence of abiotic factors in different spatial and temporal scales were made. Sampling was carried out in two seasons: between September and November 2016 (spring), and between April and July 2017 (autumn). In total, 17,146 individuals were sampled (larvae of last instars and pupae), which resulted in the identification of eleven Simuliidae species. The most abundant species were Simulium pertinax Kollar (77.55%), followed by Simulium incrustatum Lutz (14.56%) and Simulium subpallidum Lutz (2.35%). Regarding the identification of indicator species, S. pertinax, Simulium jujuyense Paterson & Shannon, S. subpallidum and Simulium orbitale Lutz stood out in mouth stretches, and Simulium rubrithorax Lutz in source stretches. Environmental variables such as conductivity, altitude, canopy cover and stream width were interpreted as important conditioning factors for the distribution of simuliid immature stages. In general, we concluded that Simuliidae are more abundant during spring in the study area, mainly downstream. This information may contribute to the implementation of efficient measures to control species of health importance in southern Brazil.