The knowledge of the natural dynamic of the biological communities in fluvial systems is relevant for the conservation of these complex ecosystems. The San Pedro River, located in the South of Chile, is a system that has a high naturalness due to the absence of significant anthropogenic intervention. In systems under a natural dynamic like this one, the flow regime determines mostly the habitat dynamics, affecting also the species distribution. This generates highly dynamic assemblages at the spatial and temporal levels. Hence, we studied the fish community structure along three hydrogeomorphological zones of the San Pedro River, named macrozones, to understand the natural dynamic of the freshwater fish communities. In addition, we analyzed the temporal dynamics of the fish assemblages in order to know structural changes between high and low flow seasons, associated to the dynamic of floodplains. Periodic fish samples were done in the San Pedro River during two annual cycles (23 months) to determine the spatial-temporal patterns, and to asses classic diversity indexes and clustering analysis based on similarity. Complementarily, fish samples were collected in different places of the basin to compare the three macrozones occurring in the river and to determine the degree of singularity of the system. The results suggest the occurrence of different fish assemblages along the river, mainly between the macrozone 1 and 2, due to the predominance of lentic habitats in the first one and large rapids in the second one. Temporarily, the augment in rainfall cause flooded habitats in dry land areas, increasing the extent and heterogeneity of the river habitats. This produces a reduction in the fish species' abundance and diversity during the high flow season. In contrast, shallow environments are dominant during the low flow season, and there is an increment both in the number of individuals and in the specific richness. The San Pedro River's ichtiofauna differs in composition and structure to those in other sectors of the basin, which makes it a highly singular ecosystem.