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Substrate heterogeneity and biofilm colonization in streams vary across both time and space, but their relative contribution to reach-scale nutrient uptake is difficult to partition. We performed multiple short-term nutrient additions over a 4-mo colonization sequence in 4 small, groundwater-fed, experimental streams. We quantified the influence of substrate size (pea gravel vs cobble) and heterogeneity (alternating sections vs well mixed) on the uptake of NH4+, NO3(-), and soluble reactive P (SRP) and transient storage properties. In general, the effect of benthic substrate on uptake velocity (v(f)) and areal nutrient uptake (U) were inversely related to substrate size, and both metrics were highest in the stream lined with pea gravel, lowest in cobble, and intermediate in streams with alternating and mixed substrates. Substrate trends were consistent among solute types, but the magnitude of uptake differed. Uptake generally was higher for NH4+ than for NO3- and SRP in these open-canopy systems. Algal biomass controlled temporal patterns of nutrient uptake but reduced exchange of water between the stream channel and transient storage zone (k(1)) such that k(1) decreased as nutrient uptake increased. Our results uniquely demonstrate that substrate heterogeneity and substrate-specific biofilms interact to influence biogeochemical cycling in streams, with implications for the role of substrate in restoring ecosystem function in impaired systems.