1. Farming Pollution
Fertilizers runoff into waterways surrounding farms. These nutrients cause problems because they allow for algae to grow. The algae blooms in very large amounts and live off these nutrients. While they eat they take up oxygen that is necessary for the plants and aquatic organisms that live in the rivers. This is a problem because the amount of oxygen in the water can drop so low that fish start to die.

2. Herbicides and Pesticides
Herbicides and pesticides will also run off the land into the nearest water way during rainfalls.
Once in the water system they act as poison to the aquatic plants and organisms.
In large enough amounts they can even kill large amounts of aquatic life.

3. Sedimentation/Erosion
During rain events not only do pesticides and fertilizers enter the rivers, but the soil from the fields also run off the land.
Once in the river the soil can cover fish spawning grounds and adds to eutrophication of lakes (pre-mature filling in of lakes).