Densification of cities and urban population contributes to increased runoff and suspended solids and alteration of the urban water cycle. Nowadays, Blue-Green Infrastructure is promoted to increase a city’s resilience to floods; however, stormwater drainage systems, supported with retention tanks are still important in protecting urban areas against floods. Sediment accumulation in stormwater infrastructure relates to an issue of pollutants such as heavy metals, nutrients etc. Research on the origin of the pollutants associated with the suspension and ultimately sediment accumulated in sewage can bring new insights about processes in urban catchment areas. This is the first study, which is focused on the analysis of stable carbon and nitrogen isotopes in bottom sediments collected from municipal retention tanks to verify the origin of the deposited pollutants immediately after pluvial floods. The research was additionally extended with water quality analyzes immediately after three types of weather: a dry period, typical precipitation (< 30 mm) and torrential rainfalls (2 events with daily precipitation over 30 mm which caused pluvial flooding of the city area). Analyses of sediments indicated that the main source of carbon and nitrogen in the bottom of the retention tanks had been brought with stormwater runoff from the city area. Organic nitrogen fertilizers appeared to be the main source of nitrogen, while the sources of organic carbon were mixed: C3 land plants, wood, and oil. Additionally, it was found that torrential rainfall caused a 23-fold increase of N-NO3concentration, a sevenfold increase of P-PO4concentration, and an over fivefold increase of concentration of organic matter, in comparison to typical precipitation.