South Wales in the UK is a region in which a densely populated south-facing coastal strip lies beneath the extensively grazed upland pastures of the Brecon hills to the north. We sampled Taff river water from just upstream of Cardiff over a period of a year (2001-2002). Thirty one of 96 (32.3%) water samples were IS900 PCR positive. The occurrence of positive samples was significantly related to rainfall on each of the preceding 6 days. Twelve (38.7%) of the PCR positive samples cultured, grew typical colonies of MAP after 8 to 11 months of incubation. They were all bovine strains of MAP and were further confirmed by MIRU typing. All were IS900 PCR positive with amplicon sequences showing 100% identity to the reference sequence in the database. By contrast, only 3 of 19 amplicon sequences from IS900 PCR performed directly on river water DNA extract were 100% identical to database; the remaining 16 all showed a conserved single nucleotide polymorphism at position 214. This has not been described previously and is consistent with the presence in Taff river water of a different strain of MAP which was unculturable by the methods we used. Sediments from 3 of the 4 reservoirs controlling the upper catchment of the Taff tested positive for MAP by IS900 PCR or by culture which equates with their deposition over at least 50 years. A previous epidemiological study reported a highly significant increase in the incidence of chronic enteritis of the Crohn's disease type in 11 of 25 electoral wards in the city of Cardiff. The leeward (north-east) bank of the river Taff as it runs through Cardiff was continuously bordered by wards with a high-incidence of Crohn's disease, but the windward (south-west) bank had a gap in high-incidence wards in the centre. We present an enhanced topographical relief map of the city which shows that this gap on the windward side of the Taff as it runs through Cardiff is directly opposite a valley open to the prevailing south-westerly winds. This would influence the distribution within Cardiff of aerosols carrying MAP from the river Taff.Our continuing studies on MAP distribution in separate catchments have shown similar associations with rainfall and that a number of sources contribute to its presence in rivers.