Display omitted •Isotope-based assessment of water cycling in a lowland, peri-urban catchment.•Higher stream evaporation and depletion of groundwater storage after two dry years.•Stream flow dominated by groundwater and waste water effluents.•Limited influence of precipitation and urban storm runoff.•Overlapping isotopic signatures in effluent and groundwater increased uncertainty in water source and age assessment. In peri-urban catchments where treated wastewater effluents are released into surface waters, knowledge of water sources and partitioning is important for mitigating water quality impacts, particularly during warm and dry periods with low discharge rates. Useful tools for the identification of water sources and flow paths under different wetness conditions are isotope tracers. However, very few studies have been carried out so far in urbanized catchments with complex land use distributions where natural headwaters interact with engineered components, e.g. effluent discharge. We undertook spatio-temporal sampling of isotopes, combined with water quality measurements, to complement climatic and hydrometric data across the 220 km2 peri-urban Erpe catchment near Berlin and assess seasonal changes in water sources during two exceptionally warm and dry years (2018 and 2019). The study showed a deterioration of water quality downstream of two municipal wastewater treatment plants; and the depletion of groundwater storage, along with isotopic enrichment of the stream, in summer 2019 (the second consecutive year with above-average temperatures and marked precipitation deficits). Streamflow in the upper reaches of the catchment was dominated by groundwater-fed tributaries in winter, but became increasingly dominated by wastewater in summer. In the lower catchment, flows were dominated by effluent from a large wastewater treatment plant, especially in summer. Young water from precipitation and urban storm runoff accounted for < 10 % of streamflow, despite the catchment being ~ 20 % urban. Similarities in the composition of wastewater and other runoff sources resulted in high uncertainties in end member separation and highlight the need for monitoring of other tracers to better characterize water impacts. Given climate change projections for the region are for drier, warmer summers, wastewater is likely to become a more dominant component of streams, which may have implications for environmental quality and ecosystem services.