Escherichia coli bacteria grow and thrive in the digestive tracts of warm-blooded animals - dogs, cats, cows, sheep - and humans. The bacteria are relatively easy to test for, so E. coli is used in water quality testing as an Faecal Indicator Organism (FIO) - in that it indicates that faecal material exists in the water, and in what concentrations. What it doesn’t indicate is where this faecal material comes from.
In British rivers, there are two main sources of E. coli: agriculture and sewage.
Many strains of E. coli are harmless to humans - the principal harmful strains (Shiga Toxin E. coli or STEC) are mostly present in cattle. This doesn’t mean that human-originated E. coli is a good sign: alongside the E. coli from sewage there are organisms like norovirus and salmonella.
Heavy rainfall has a double-impact on E. coli in rivers: as well as storm overflows from sewage infrastructure, the rain carries agricultural run-off from fields and farms, washing faecal material from pastures into the nearby rivers.
But heavy rainfall is not the main problem, if, even in dry weather, faecal organisms in rivers far exceed official safe swimming levels.