Loose deposits have a significant influence on drinking water quality in distribution networks. Thus, there is a need to develop fast and effective methods to analyze bacterial abundance in these sediments. Techniques for detachment of bacteria from particles have previously been optimized for soil and streambed sediments. In this study we investigated the applicability of density gradient centrifugation method for separation of bacteria from deposits in drinking water networks for subsequent counting with flow cytometer. The study was carried out in lab scale using Escherichia coli and Bacillus subtilis as a model organisms for Gram positive and Gram negative microorganisms and Goethite as a model for loose deposits. Both low and high speed density gradient centrifugation methods were inefficient for separation of bacteria in the presence of Goethite due to strong affinity between the cells and oxides. However, flow cytometry was efficient for counting bacteria after treatment of water samples using density gradient centrifugation in the absence of Goethite.