Comprehensive monitoring of pesticide accumulation in Flathead waters is not currently done. We do know that the amount and frequency of pesticide use around Flathead Lake has increased due to increased use by orchards. Weed and insect problems in forests and on farmland throughout the watershed are also leading to increased pesticide use. How much finds its way into the water is unknown. Erosion on agricultural lands, logged forests, and river and stream banks contributes the largest proportion of pollutants by volume.
Sediment can harm aquatic organisms including fish.
Sediments also carry nutrients and other pollutants in the eroded soils. The burning of fossil fuels is a major source of nitrates, sulfates and heavy metals such as lead, mercury and cadmium. Cars and trucks, as well as burning from many sources, contribute to airborne pollution in the Flathead. Watercraft engines are very polluting. Pesticides and herbicides enter the air during aerial or aerosol applications.