Nature-based solutions (NbS) are increasingly recognized as vital components of sustainable urban projects aimed at improving human well-being and biodiversity. In urban areas with insufficient sanitation infrastructure, greywater often flows into nearby streams via stormwater drainage networks, exacerbating water quality issues. This study assesses the impact of green infrastructure on water quality of a headwater creek (San Francisco stream), located in the Metropolitan Area of Buenos Aires, Argentina. We analyzed greywater discharges entering the stream across seasons during July 2019– Febrary 2020, classifying stormwater drainage systems into vegetated ditches and concrete channels (n = 15 for both). Linear models showed that seasonality and infrastructure type had independent and differential effects on effluent quality. Grey infrastructure led to a significant increase in flow entering the stream across seasons compared with vegetated ditches, accompanied by a reduction in nitrate and total phosphorus levels. In turn, winter showed elevated BOD and COD levels, while summer experienced increased DOC and nitrate concentrations. Bayesian models indicated that during the observed critical season (winter), grey infrastructure caused a more substantial organic load impact, with pollutant increases ranging from 3–96% compared to green infrastructure. Furthermore, biofilters (n = 7) installed at urban drainage outlets during 2021-2022 were moderately effective in reducing pollutant levels, removing 2–84% of BOD and COD, 13–92% of DOC, and 2–39% of DIN entering the stream. These results highlight the ecological advantages of NbS in urban water management, demonstrating the potential of green infrastructure to improve water quality, enhance biodiversity, and strengthen the resilience of urban ecosystems.