A space-for-time substitution approach was used to evaluate potential effects of climate change on stream nutrient uptake by examining the relationship between stream environmental parameters and carbon (C), nitrogen (N) and phosphorus (P) uptake along an altitudinal gradient. The study was carried out in 14 streams located in the Central Pyrenees (NE Spain) draining calcareous catchments that cover an altitudinal range of 700–2,100 m a.s.l. In these streams, uptake of inorganic (soluble reactive phosphorus (SRP), ammonium and nitrate) and organic (acetate and glycine) nutrients was estimated. Additionally, several physical, chemical and biological parameters were measured. Results showed higher uptake for both SRP, a potentially limiting nutrient in these streams, and glycine, a labile source of dissolved organic N, than for the rest of the nutrients. Uptake of SRP, nitrate, glycine and acetate varied along stream environmental gradients associated with changes in stream hydromorphology, SRP availability and epilithic biomass. However, these gradients did not vary with altitude. These results indicate that climate change effects on stream nutrient uptake are more likely to be driven by indirect effects on hydromorphology and nutrient availability induced by shifts in the precipitation and run-off regime than by direct modifications in the thermal regime.