Here in the UK there are four primary causes.
1) Sewage. Historically some rivers (even the Thames) have been used to carry away human waste, whilst that is no longer the case, there are occasional "spillages" from historic infrastructure into rivers.
2) Industrial pollution. River water is used in many industrial processes. Whilst it is illegal to pollute water as a consequence of such production, there is little doubt that it still happens.
3) Agricultural runoff. This is the most problematical source of pollution. Agricultural chemicals, and animal slurry find their way into water courses.
4) Illegal dumping. Sometimes naughty people dump things into rivers as a cheap mechanism for disposal.
