Heavy metals comprise one of the most hazardous groups of pollutants entering the aquatic environment. Their behaviour and ecotoxicological effects are not well understood especially if they are occur as a mix of metals. Drawing on data from three Prague creeks, the paper illustrates changes in heavy metals bioavailability resulting from different environmental conditions and related differences in urban drainage types. Heavy metals in sediment from creeks impacted by stormwater drain discharges are more bioavailable and accumulate in organisms to higher concentrations than in organisms from creeks affected by combined sewer overflows. The results also show that bioassay levels of lead in fish from the creeks exceed acceptable concentrations for human consumption (EC 466/2001) and therefore represent a potential health risk for humans. The results demonstrate the importance of providing improved interception efficiency in the drainage system structures. In particular, a higher level of interception of fine particles is critical, because of their higher metal adsorption capacity than for coarser particles.