The discharge of high flood water (2010) into reservoirs located in the Upper Vistula River catchment and into the overloaded Vistula River channel may strongly affect water and sediment quality. To investigate the contamination of the flooded area in the center of Cracow, total of 32 sediment samples were collected along the length of the Vistula River and also from the cross section in the floodplain area. Additionally, 12 samples of the flooded sediments were collected along the Wilga River – a tributary of the Vistula located within the investigated area. The concentrations of Zn, Pb, Cd, Cu, Mn, Zn, and Fe in the bulk samples and size fraction <20 μm were studied. The metals concentration in the Vistula River flood sediment samples varied in wide ranges (mg/kg): Zn 59-1013, Pb 17-263, Cd 2.6-23, Mn 145-469, and Fe 0.70-3.59%, and was considerably higher in the size fraction samples. The concentration of Cu was low and reached up to 40 mg/kg. The highest amount of Zn was found in the sediment sample from the cross section, located 38 m from the Vistula River channel. Three-step sequential extraction revealed the most mobile metals in the sediment fraction <20 μm, which were as follows: Cd (77% of the total amount), Pb (55%), and Zn (42%). The contamination of the Wilga River flood sediments was lower when compared with Vistula River contamination.