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Simplification of natural habitats is a growing global concern demanding that ecologists better understand how habitat heterogeneity influences the structure and functioning of ecosystems. While there is extensive evidence that physical habitat heterogeneity affects the structure of biotic communities (i.e., organismal abundance, distribution, diversity, etc.), ecologists know little about how variability in physical conditions within habitats regulates ecological processes that are important for the functioning of all ecosystem. We performed a field experiment to assess the effects of geomorphic heterogeneity (i.e., variation in substrate size) on rates of benthic productivity and respiration at the scale of whole riffle habitats in a stream ecosystem. While holding median sizes constant, we manipulated variation in the size of stream bed sediments in replicate riffles to create two treatments representing increased and decreased levels of physical habitat heterogeneity relative to natural conditions in the stream. Physical habitat heterogeneity had an immediate and significant impact on the primary productivity of stream algae and oil the respiration of the benthic biofilm. The rates of both ecological processes were elevated in the high-heterogeneity riffles, probably as a result of quantified alterations to near-bed flow velocity and turbulence intensity. Results presented here provide Support for the widely held, but largely untested, assumption that physical habitat heterogencity exhibits control over ecosystem-level processes, and it suggests that human-induced simplification of habitats may indeed be altering the functioning of ecosystems.