While purified bacterial cells and DNA – the signature of life – from soil and sediment matrices have been extensively studied in a wide range of environments and in different microbial ecosystems, the paucity of data on DNA extraction from contaminated sediments emphasizes the need for further research on the isolation and quantification of bacterial cells and DNA in sediments. Consequently, the Nycondez gradient centrifugation method was applied to extract bacterial cells from contaminated and uncontaminated sediments. Quantitative estimates of recovered bacterial cells were obtained from direct counts performed using DAPI (4′,6′-diamino-2-phenylindole hypochloride) staining couples with fluorescence microscopy and indirect counts (colony-forming units). The estimation was improved by using an efficient method of comparing sediment types composed of quantifying bacterial densities in three steps: S1 the initial freshwater sediments; S2 the first supernatant recovered after mixing the sediments with sodium hexametaphosphate solution followed by centrifugation; and S3 the extracted cells. Total and extracellular DNA were extracted and quantified in each of the three steps. Additional analysis of faecal indicator bacteria (FIB) including E. coli and Enterococcus (ENT) was also performed in each step. The results display considerable variability in the quantity of bacteria cells depending on sediment type, ranging from 1.2 × 105 to 6.2 × 109 cell g−1 dry sediments. The treatment with sodium hexametaphosphate solution (2%) leads to the desorption of bacterial populations which were firmly adsorbed on contaminated sediment surfaces resulting in more than 90% of the FIB being recovered. The Nycondez density gradient centrifugation method makes it possible to extract bacterial cells from freshwater sediments without extracellular DNA so it is ideal for metagenomic analysis of bacteria.