Recently, a functional gene array—GeoChip—was introduced, targeting more than 12,000 different microbial functional genes. In addition to microbial genes involved in widespread microbial functions, this array also includes 37 probes for genes involved in atrazine [6-chloro-N-ethyl-N′-(1-methylethyl)-1,3,5-triazine-2,4-diamine] degradation. In our study, we evaluated whether this type of microarray is suitable for screening a rural aquifer for native atrazine degraders and their intrinsic degradation capacities. Surprisingly, small amounts of organic contaminants (up to ∼10 μg/L) in a well close to a farmyard led to the establishment of a specific degrader community. This means that although contamination at such low concentrations should have only a minor effect on water quality, the microbial community in this oligotrophic environment reacted in a very sensitive manner to the contaminants. Specific atrazine degradation genes were detected in the aquifer showing the highest level of contamination. Their presence was confirmed using a specially developed polymerase chain reaction approach combined with gene sequence analysis. Whether this should be considered an undesired ecotoxicological effect or whether it should be taken as evidence for regular natural attenuation of such diffuse contaminants is a question that remains to be answered by more comprehensive studies.