Fluvial geomorphology provides an initial starting point for characterizing and understanding the ecogeomorphology of river networks. Knowledge of the spatial organization of morphological features and the way they influence processes within river networks is important for identifying potential links between the physical and ecological character of river systems. Here, a top-down geographic information system-based approach for determining the physical typology of river networks was used to determine and characterize the functional process zones (FPZs; large tracts of the river network with similar hydrogeomorphological character) of two rivers in central Chile. Seven distinct FPZs emerged from the analysis, and these had a nonuniform distribution along the river networks of the Biobio and Imperial Rivers. Some FPZs were frequent in number, with each FPZ segment being variable in length, whereas others were short and represented in limited number. A strong association between the physical character of FPZs and fish community was shown for the Biobio and Imperial Rivers. Specifically, dominant fish species varied among FPZs, and their habitat preferences were strongly related to the hydrogeomorphic character of the FPZ they dominated. These results are significant, as they can inform design of future ecological research and development of effective monitoring programmes.