While in their 4-6 year larval stage lamprey occupy a special niche in the stream system, filtering microscopic plants and animals from the bottom sediments. They fall prey to a wide variety of species including trout, crayfish, and birds. Lamprey have similar freshwater habitat requirements as do some of the Pacific salmon, therefore they have encountered similar habitat problems. Though absolute historical population sizes of the lamprey are not known, it is clear that the fish, once a significant tribal subsistence food, have shown severe decline. Historical splash damming has scoured many of the stream bottoms down to bedrock, removing necessary habitat.
Dams can hinder adult and juvenile passage or completely cut off prime spawning habitat.
Inappropriate logging and grazing practices can alter stream flows and degrade habitat severely. The first 4 to 6 years of the Pacific lampreys life are critical times. Animals that filter water and mud for food are very susceptible to pollutants in the water column and sediments. Lamprey may be impacted by pollutants from urban and agricultural runoff that can concentrate in the sediments. Because this species depends on muddy bottoms, backwater areas, and low gradient areas during its juvenile life stage, it is susceptible to loss of wetlands, side channels, back eddies, and beaver ponds resulting from agricultural, forestry or urban development practices or channelization for flood control.