I suspect that the writer was confusing disease with pollution. In the
US agricultural runoff has caused severe problems for fish - feed lot
slurry, chemicals, and silt, for example. Less obvious is the effect on
temperature regimes. But none of this is really a disease problem - at
least a major one.
Similarly urban runoff pumps all kinds of bad stuff into streams,
estuaries, lakes, and bays, some of which might induce or exacerbate
diseases, but most of it simply poisons our finny friends (and sometimes
us!). In my part of the world the problem is worsened by coupling sewer
systems and storm drains.
One possible culprit - salmon net pens discharge a lot of waste, and may
transmit diseases to wild stocks (an vice versa).