A central tenet of river science is the interaction between flow and the physical habitat template—hydrogeomorphology—that governs biophysical structure and function. While studies have shown how this interplay shapes structural river ecosystem attributes, our knowledge of their influence on ecosystem function is limited. Using geomorphological, hydrological, and stable isotope ratio data for basal resources and primary and secondary consumers from 88 rivers, we test hypotheses on relationships between hydrogeomorphology and food chain length. A significant curvilinear relationship between the physical heterogeneity of a river reach and food chain length was found. Low flow variance was shown to have an additive influence on food chain length; longer food chain lengths occurred in reaches that experienced permanent flow but not the frequency of overbank floods. Ecosystem size had no effect on food chain length. The results of this study suggest reach-scale hydrogeomorphology has a direct influence on ecological function—food chain length—in riverine landscapes. We suggest that the spatial heterogeneity of physical character is a primary driver of ecosystem function that provides a template upon which flow variability acts as a regulator of food chain length. Understanding biocomplexity, the interplay of spatial heterogeneity and temporal variability, is critical to predicting responses of riverine landscapes to natural and human-derived disturbances.