We studied the effect of point-source and non-point-source pollution on the retention capacity of the stream and its link with the metabolic state (primary production and respiration) and invertebrates assemblages in a third order Mediterranean stream. Two experimental sites were chosen: one in the upper part of the catchment (Montégut site) characterized by low concentrations in nitrate and phosphate and one in the lower part of the catchment (Lézat site) characterized by high nitrate and phosphorus concentrations. Both experimental sites were located on reaches that included a Waste Water Treatment Plant (WWTP) point nutrient source allowing discussion of the relative effects of point-source and non-point-source nutrients loads on ecosystem function (respiration and uptake rates) and aquatic organism assemblages. NH4
+-N, and PO4
−-P uptake rates were determined using solute additions conducted at constant rates (short-term nutrient addition procedure) and NO3
−-N uptake rates were determined using instantaneous solute addition (slug addition procedure). Rates of gross primary production (GPP) and ecosystem respiration were determined using the open system, two-stations diurnal oxygen change method. Benthic invertebrate communities were investigated for species and functional feeding groups diversities measurements. Results show that autotrophy in the river results from nutrients of two distinct origins: point sources for phosphorus (urban area and WWTP) and non-point sources for nitrogen (agricultural zones) with local additions from WWTP inputs. Comparison between the two sites shows that the WWTP did not affect uptake rates, respiration or primary production of the ecosystem in the low-nutrient Montégut reach despite increase of invertebrates communities biomass density. Inputs from the WWTP, in the high nitrate and phosphate Lézat reach, increased respiration, lower benthic biomass and led to changes in the species composition and did not affect uptake rates.