The brown food chain (based on decomposers) co-exists in streams with the green food chain (based on primary producers). The two trophic chains perform specific ecosystem functions which may be altered by the effect of contaminants. Copper is a common contaminant with recognized effects on several compartments of the two trophic chains. We applied it in two separate mesocosm experiments, in which we tested the effects of copper after contrasting patterns of contaminant exposure (constant vs hump-shaped). The constant input simulated a chronic contamination (average of 20 μg/L Cu), while the hump-shaped simulated the steady arrival of copper, the occurrence of a peak (reaching ca. 60 μg/L Cu), and its progressive decrease (down to 10–15 μg/L Cu). In the green trophic food chain, copper exposure decreased the total chlorophyll-a as well as the basal fluorescence and the photosynthetic yield. The treatment receiving hump-shaped inputs caused the highest mortality of the green food chain consumer, the snail Radix balthica. In the chronic copper exposure, mortality achieved a maximum of 80% by the end of the experiment but occurred later than that in the hump-shaped treatment. Effects on the brown food chain were not so pronounced; the microbial decomposition rate of leaflitter decreased nearly ca. 50% after 14 days of copper exposure. Effects on decomposition translated into the ingestion performance of detritivores, which decreased in the two copper treatments. Our results provide evidence that copper affected the two trophic food chains. The hump-shaped arrival included a peak of high concentration, which caused lethal effects on the consumers, but also a decreasing limb, which allowed a partial recovery of the algal photosynthetic variables. Our results suggest the need to consider the different compartments and functions performed within the stream trophic web when evaluating the effects of a contaminant in a river ecosystem.