The Species Sorting concept, one of the models developed to explain patterns in metacommunity structure, suggests that relationships between biological communities and environmental conditions is the basic means of the species selection processes. A second concept is neutral theory, and the idea of neutral dynamics underpinning metacommunity structure, cannot be overlooked. The third mechanism is the Mass Effect concept, that focuses on the interaction between environmental condition and neutral effects. In the present study, we partitioned fish communities in streams between niche and neutral theory concepts, identifying the best representation of metacommunity structure, and assessed if linear and hydrographic distance were equivalent in the representation of neutral processes. The result points to the importance of species sorting mechanisms in structuring fish communities with neutral processes best represented by the linear distances. On the other hand, the best representation of species’ niches was achieved with average values and variance of the local conditions.