Paper makers pay substantial amounts for controlling biofouling and microbial contamination of their facilities. When successful anti-fouling strategies are in place, these costs are justified by improved paper quality and reduced operating costs. Two contamination scenarios are conceivable in a paper mill: (1) Transport of high pulp- and water volumes through the plant leads to high migration rates of microorganisms and consequently to the spread of related bacterial communities in all areas of the plant. (2) Environmental conditions select for adapted communities in unit operations, independent of volume flows. These two scenarios have major implications for treatment strategies. We follow bacterial communities using Single Strand Conformation Polymorphisms of PCR-amplified bacterial 16S rDNA. Two sets of bacterial communities along the production lines could be detected. Within the sets, the communities are related to each other. Between the sets, the relatedness of the communities is weak. When following pulp flow in the paper mill, the disconnect between the community sets coincides with two samples from the entry and exit of one specific storage silo for pulp. Bacterial communities in this storage silo have undergone a dramatic shift, possibly because of a strong selection for a locally adapted community as hypothesized in scenario (2). A long retention time in the silo facilitated growth of this community to sufficiently large numbers to outweigh the entering community. Bacterial communities downstream the silo are more related to each other, possibly following contamination scenario (1). Treatment upstream of the storage silo will not affect downstream communities as the silo divides the paper mill into two separate entities from a bacterial perspective. A chronically contaminated storage silo is comparable to an infection of an implant or a lung in that the source of the infection has to be treated rather than the contaminated bloodstream or the pulp circuit.