Agriculture can cause soil erosion due to the physical disturbance of soil and vegetation during ploughing, overgrazing, logging and road building. This affects the murkiness and the amount of salts and minerals in water when run off from the land enters water courses.
This can cause increases in nutrients due to fertilizers and excreta entering the water systems and contributes worrying amounts of nitrates and phosphates to water bodies. These chemicals can cause eutrofication in rivers, dams, lakes and estuaries.
Increased pesticide use, which land up in our water sources can also damage the water ecosystems by killing the animals that live in the water.