Our paper presents the results of heavy metal (HM) (Zn, Cu, Pb, Cd) content in bottom sediments from retention tanks along Oliwa Stream in Gdańsk, Poland, before a flood (BF) and after a flood (AF) 14-15 July 2016. The flood had a huge impact on the quality of bottom sediments and their displacement. The concentrations of HM differed significantly for research series conducted 3 months BF and 8 months AF. The concentration of Cu increased from 3.5 mg/kg to 88.8 mg/kg BF and from 12.1 mg/kg to 1,114.3 mg/kg AF, Zn from 27.4 mg/kg to 129.9 mg/kg BF; and 42.3 mg/kg to 244.8 mg/kg AF, Cd from 0.04 mg/kg to 0.47 mg/kg BF, and 0.08 mg/kg to 0.47 mg/kg AF. Also, the migration of some metals, mostly Cu to retention tanks located downstream, was observed, resulting from the washing away of sediments in the upper part of the stream. Since the stream inflows to the Gulf of Gdansk, urban flooding created a risk of migration of contaminants to the Baltic Sea.