AbstractWe examined how communities of macroinvertebrates occurring in functional process zones (FPZs) are affected by the location of FPZs in the river continuum. We delineated FPZs for three rivers displaying significant disparities in elevation, annual precipitation, valley shape, and other valley‐scale hydrogeomorphic variables. We extracted corresponding macroinvertebrate community data from the US National Water Quality Monitoring Council database and matched it to the stream order (SO) and FPZ delineations. We examined community structure in the three rivers by partitioning the variances associated with the FPZ and SO delineations. Then, we examined community variation as patterns of beta‐diversity for communities of FPZs in different SOs. In total, 23 FPZ‐SO configurations were examined. SO and FPZ delineations contributed similarly to the variance in the structure of macroinvertebrate communities. Taxa turnover accounted for the majority of the compositional change in communities of FPZs along the river continuum, while the functional composition showed primarily a nested structure. Pairwise comparison of communities for each FPZ along the river continuum showed that significant differences in community composition occurred at high SO in the three examined rivers. In this manuscript, we show that communities of FPZs are only partially comparable along the river continuum as significant compositional changes occur when comparing communities of FPZs in distant SOs. We bring, therefore, new elements to improve the interpretation of the River Ecosystem Synthesis concept that can have wider implications for understanding the biocomplexity of hydrogeomorphic patchiness in river networks.