Prior to 1850 the midwestern U.S.A. was covered by tallgrass prairie, emergent wetlands and riparian forests. There were fewer headwater streams because the soil-plant system was a large sponge and a "living filter". Intensive row crop agriculture has produced many sources of non-point source (NPS) pollutants such as sediment, fertilizers, pesticides, and herbicides.
Other factors leading to sediment increase in streams are cropping to stream edge and allowing livestock to graze the edges of streambanks. Both make streambanks unstable.
Edge cropping makes streambanks unstable because roots of riparian plant species that were there year-round are replaced with seasonal crops such as corn or soybeans. This means there are not roots holding the streambank up for a large part of the year.
Grazing to streambank edge also leads to erosion and sediment loading in streams. Livestock break streambanks apart making the soil more unstable while also compacting certain areas leading to decreased plant growth that would help hold streambanks together.
Fertilizers, pesticides, and herbicides all are applied to manage crop growth. Many of these chemicals can end up in stream water during rains by runoff on the top of the soil, or by bypassing riparian zones in drainage tiles.
The result of these management techniques is a stream system with rapid runoff, deeply inscised channels with eroding banks, a lowered water table, and stream water with higher chemical contents.