Heavy metals are widespread pollutants with significant environment risk due to high toxicity and clear tendency for accumulation in different matrices – soils, sediments, biota. The main research objective of this work is to assess the impact of heavy met al pollution on key structural and functional parameters of microbial communities in sediments of river -dam sequence of small hydropower cascade Middle Iskar, Bulgaria. The content of heavy metals (As, Cd, Cu, Hg, Pb, Zn) was measured during the low water summer periods of 2012, 2013 and 2014. The evaluation of site quality and heavy metal pollution was done by use of one integrated index - Pollution Load Index and it was compared to total count of sediment microbiota and count of coliform bacteria, also with total dehydrogenase activity and index of phosphatase activity. The assessment of heavy metal pollution in river -dam sequence of cascade indicates the higher metal concentrations and high Pollution Load Index in dam sediments. At low level of pollution in river sites, the both structural and functional microbial parameters react to local variations of heavy metal concentrations and high negative correlation (r= -0.8÷-0.9) exists between variables. But in dam sites, the microbial community is more resistant to pollution and structural parameters react conservatively with long reaction time. The enzyme activities are more adaptive and sensitive indicators for different level of environmental impact in this case. The complex phosphatase and dehydrogenase activities have a high potential to be used as reliable parameters for precise assessment of hazardous sediment pollution in complicated ecological situations with cumulative impacts.