Wastewater treatment plant (WWTP) effluents alter water chemistry and in-stream nutrient uptake rates of receiving freshwaters, thus changing the magnitude and fate of the nutrients exported. In Mediterranean regions, the dilution capacity of receiving streams can vary strongly over time due to the seasonal occurrence of floods and droughts, causing temporal variability of nutrient uptake. We assessed the temporal patterns and the controlling factors of net nutrient uptake in an intermittent Mediterranean stream receiving WWTP effluent inputs. We compiled the longitudinal concentration profiles of ambient dissolved inorganic nitrogen (DIN) and soluble reactive phosphorus (SRP) along a 800 m reach on 47 sampling dates between 2001 and 2017, encompassing a wide range of hydrological conditions. We estimated net nutrient uptake in the receiving stream. In 72% of the dates, high rates of net ammonium uptake co-occurred with net releases of either nitrate or nitrite. This pattern suggests that the receiving stream has a high nitrification capacity. Conversely, 75% of the dates did not show any longitudinal pattern in SRP concentration, suggesting that uptake and release processes for this element were either counterbalanced or both occurred at very low rates. ... mehrFinally, net ammonium uptake was low when the stream had a low dilution capacity (< 40%) and ammonium concentration was high. Overall, we demonstrate that consideration of the receiving stream’s dilution capacity is imperative to the management of freshwaters to guarantee an adequate dilution of WWTP effluent inputs and avoid saturation of in-stream nutrient uptake capacity under low flow conditions in urban landscapes.