Well biofouling is a complex and not yet sufficiently understood process. Water wells represent a unique habitat, since they create a link between the anaerobic ground water containing Fe(II) and the aerobic surface. This groundwater is rich in soluble Fe(II) and the presence of trace amounts of free oxygen in the well screens presents ideal conditions for the growth of iron bacteria. The ochreous deposits produced block not only the filter area, but also the adjacent gravel pack or even parts of the aquifer, and result in a steady decrease of well performance. In this project, the bacterial communities of several Berlin wells have been compared using standard microscopic techniques and molecular techniques like DGGE. The aim of this study is to identify the responsible bacteria and associated processes that lead to well clogging. The sampling system allows easy and effective collection of undisturbed biofilm samples with minimal impact on normal well operation. Fingerprinting analysis indicates the presence of bacterial populations that are ubiquitous in the wells and certain indicator bacteria which can be found in only few wells. Free water and biofilm populations show distinct similarities. Some well populations can be grouped in clusters, depending on the location of the well. Further comparison with chemical data of the wells is planned to asses the impact of chemical conditions of the respective groundwater on the bacteria responsible for clogging. A sampling device was designed and built for exposure of carrier materials into different Berlin drinking water abstraction wells. In addition, samples from well components (pumps and pipes) and water samples were collected. The DNA was extracted using the FastDNA SPIN Kit for Soil (MP). 16S rDNA polymerase chain reaction (PCR) of the V3 region and denaturing gradient gel electrophoresis (DGGE) analyses were performed on the DNA samples (Muyzer et al., 1993).