Bacterial induced well clogging is a common problem in water wells. The well represents a unique habitat by creating a link between the anaerobic ground water, containing Fe(II) and the aerobic surface. The presence of trace amounts of free oxygen in the well screens, sets ideal conditions for the growth of iron bacteria (Stuetz and McLaughlan, 2004). These bacteria precipitate iron hydroxides (Cullimore, 1999), that not only block the filter area, but also the adjacent gravel pack or even parts of the aquifer and result in a steady decrease of well performance. Each well has it’s own distinct chemical conditions, which impact the type of bacterial community that forms in the gravel pack. Within this project a novel sampling system was developed, which allowed the collection of intact biofilm samples from a selected range of Berlin water wells. The resulting biofilms were microscopically examined to gain a first rough overview of the different sampling sites. Subsequently, the bacterial DNA was extracted and used for a population comparison utilizing denaturing gradient gel electrophoresis, cloning and sequencing.