Streamflow measurements from the North Fork show a systematic increase in peakflows. Because this trend is not found in the South Fork streamflow data, it suggests a relationship between land use activities more prevalent in the North Fork. Between 1928 and 1995, ten of the largest peak flows recorded by the North Fork gage occurred between 1980 and 1995. Peak flows can scour gravel beds containing salmon eggs. The scoured sediment may be re-deposited over downstream salmon redds, smothering the eggs.
Peak flows can also flush out juvenile salmon from normally quiet rearing areas.
Low streamflows are problematic in the Stillaguamish from July through September. The cumulative effect of groundwater withdrawals and loss of wetlands can also contribute to low flows. The low summer flows also permit saline waters from the Sound to move further upstream in the mainstem Stillaguamish than in historic times when summer flows were larger. Low flows can cause salmon to be stranded, limit or impede salmon migration, and contribute to a decrease in dissolved oxygen, an increase in water temperature, and an increase in the concentration of pollutants. Nonpoint source pollution is a major cause of water quality pollution in the Stillaguamish, with agricultural practices, onsite sewage disposal, development and urban runoff, and forest practices being the major sources.