Whole-stream rates of nutrient uptake and metabolism vary with season in forested headwater streams, but seasonal variation in rates at the substratum scale, which collectively generate whole-stream patterns, have not previously been quantified. We measured gross primary production (GPP), community respiration (CR), and NO₃⁻ uptake rates (NO₃⁻ U) on 7 substrata using in situ microcosms during spring, summer, and autumn in 3 headwater streams in northern Michigan. We quantified the areal reach coverage of each substratum, scaled NO₃⁻ U and metabolism to the stream reach (100 m), and compared scaled NO₃⁻ U to whole-stream NO₃⁻ U (measured using short-term nutrient additions). Patterns of GPP, CR, and NO₃⁻ U were different among substratum types and seasons. Substratum-specific NO₃⁻ U was positively related to GPP on epilithic biofilms and to CR on epixylic biofilms, bryophytes, and coarse and fine benthic organic matter (FBOM). During summer, large wood and FBOM accounted for 86% of reach-scale NO₃⁻ U, whereas epilithon contributed 28% and 49% of reach-scale NO₃⁻ U in spring and autumn, respectively. This result was unexpected for these forested closed-canopy streams. When substratum-specific rates were scaled up, NO₃⁻ U was not different from whole-stream NO₃⁻ U calculated from short-term enrichment. For large wood, organic matter, and epilithon, high molar ratios of C:N uptake suggested that NO₃⁻ uptake did not satisfy overall N demand. Streambed substratum composition influenced seasonal variability of reach-scale nutrient uptake by its influence on metabolism and changed the relative contribution of several substrata to whole-stream rates through time.