Land-use change can alter the spatial variance of carbon, nitrogen and phosphorus (C, N, P) delivery across a watershed and lead to altered nutrient limitation and export patterns. We tested the effects of land-use on C, N, and P limitation in 13 tributary and 3 mainstem locations in the Portneuf River watershed, Idaho using nutrient diffusing substrates. Impacted and nonimpacted sites were paired based on sub-basin size, impact type (minimal, agro-urban), location within the watershed, and discharge. Across all sites, regardless of impact, mean chlorophyll a was significantly stimulated (p < 0.002) by N and N+P addition and suppressed (p< 0.000) by C addition. Ash free dry mass (AFDM) did not respond to any treatment except for C+P addition. Chlorophyll a response ratios (treatment/control) were 20% lower for impacted than nonimpacted sites. Autotrophic index (AFDM/chlorophyll a) was significantly lower for N additions and significantly higher for C additions across all sites, suggesting that nutrient additions caused shifts between heterotrophic and autotrophic communities. Our results indicate that autotrophic and heterotrophic biofilm components may respond differently to nutrient additions, perhaps due to respiratory demand or competition for resources. These differences may potentially buffer or accelerate nutrient export depending on nutrient limitation status.