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The growth of biofilms on the internal surfaces of pipes in water distribution systems is well documented. When nutrients become limited or the biofilm extends beyond the laminar flow boundary layer of the system, areas of the biofilm may detach and move into the bulk of the water. These clumps of cells may, therefore, give an indication of the amount of biofilm material which is detaching into the water. However, conventional methods of enumerating bacteria by plate counts do not distinguish between single bacteria and clumps of cells. In this study, a 1.3 km-long experimental pipe rig was used to study the effect of flow rate on bacteria attached to pipe walls and in settled deposits. The study was designed to quantify the total bacteria shed from the pipe walls, present in clumps of organic and inorganic material. An epifluorescence microscopy technique was developed which allowed both individual and associated bacteria to be stained and counted. This method was initially used to establish a baseline of bacterial numbers under low disinfectant residual conditions and then to study the effect of changing the flow rate under different disinfection regimes.