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Wastewater treatment plants (WWTPs) have eliminated many problems related to sewage inputs to aquatic systems. However, the treated effluents still affect river and stream ecosystems. Yet, very limited information is available about the fate of treated effluents in tropical receiving water bodies. Here, we examined the longitudinal changes in ammonium (NH4-N), nitrate (NO3-N), and soluble reactive phosphorus (SRP) concentrations in reaches downstream from chronic WWTP inputs in three receiving rivers in São Paulo state (Southeastern Brazil). The studied WWTPs were not designed or operated to have specific tertiary treatment for nutrient removal at the time of the study. We conducted a total of five sampling campaigns between 2019 and 2021. We applied the nutrient spiraling approach to these high-magnitude nutrient additions to examine net nutrient uptake. Changes in nutrient loads along the reaches were also examined. Overall, nutrient concentrations and loads were considerably increased by WWTP discharges. Net uptake lengths (SW-net) for NO3-N, NH4-N, and SRP ranged from 1.2 to 13.6, 1.5–infinity (uptake coefficient < 0), and 1.2–7.5 km, respectively. Net uptake velocities (Vf-net) varied between 0.7–2.5, −0.4 to 4.1, and 0.2–10.2 mm/min, respectively. Areal net uptake rates (Unet) ranged from 0.78 to 10.7, −20.08–45.8, and 0.18–4.4 g/m2/min for NO3-N, NH4-N, and SRP, respectively. High export (long SW-net) and limited net uptake along the reaches (low Vf-net) indicated that nutrients were transported downstream for long distances without efficient removal (nutrient availability higher than demand) despite the high mass removal (high Unet). These results suggest that the export of nutrients is substantial, potentially creating water quality impairments to downstream ecosystems. Our study highlighted that WWTPs with limited nutrient removal have considerable effects on water chemistry, nutrient cycling and loading in tropical receiving freshwaters.