In most cases nutrients are carried into a waterbody when water drains through the surrounding rocks and soils, picking up nitrogen and phosphorus compounds along the way. For this reason, knowledge of the geology and physiography of an area can provide insight into how much nutrient enrichment can be reasonably expected in an individual waterbody from this natural source.

For example, lakes in the New Hope Ridge/Greenhead Slope lake region in northwestern Florida (in Washington, Bay, Calhoun, and Jackson counties) can be expected to have low nutrient levels because they are in a nutrient-poor geographic region, whereas lakes in the Lakeland/Bone Valley Upland lake region in central Florida (in Polk and Hillsborough counties) can be expected to have very high nutrient levels because the land surrounding the lakes is nutrient-rich.

There are many other sources of nutrients but they generally are not as substantial as nutrient contributions from surrounding rocks and soils. Some sources are natural and others are the result of human activity. Nutrients are conveyed in rainfall, stormwater runoff, seepage from septic systems, bird and animal feces, and the air itself. They may come from nearby woods, farms, yards, and streets - in other words, anywhere in the watershed.