Assess your own actions around the home and yard or farmstead and cropland. If there is a stream or lake on your property, you might want to check water quality as it enters and leaves your property. If a tile line or storm sewer drains nearby, you might grab a water sample while the water is flowing fast. This can range from immediately following a rainstorm to about 24 hours after the storm. Concrete and other paved surfaces cause water to flow faster.
Soil slows down water while it filters through to the tile line.
Others utilize the services of partners like the local water suppliers or Universities to conduct tests. Additional information can also be obtained by going to EPA's Monitoring Water Quality web site. Enlist the assistance of a reliable, locally respected watershed coordinator. You won't be able to do everything yourself. There just isn't enough time to coordinate it all.