Sub-basins in the mainstem - secondary restoration strategy group contain small rivers with floodplains that flow into the mainstem - primary restoration strategy group. These sub-basins currently support lower levels of Chinook salmon spawning or spawning potential than the mainstem - primary restoration strategy group. They contain off-channel Chinook salmon spawning and rearing areas, as well as spawning and rearing habitat for other salmon and presumed foraging habitat for bull trout (Pentec Environmental and NW GIS, 1999; Snohomish Basin Salmon Recovery Forum, 2001; Haring, 2002).

Some habitat and watershed processes are moderately degraded. Habitat problems include loss of floodplain connectivity due to dikes, bank hardening, roads, railroads, and bridges; excessive erosion of streambanks;
loss of riparian vegetation; and decreased fish passage due to human-made barriers such as culverts (primarily affecting coho). Some waterbodies also lack large woody debris and have degraded water quality due to high temperature, nutrient levels, and fecal coliform counts (Snohomish Basin Salmonid Recovery Technical Committee, 2002; Haring, 2002).

Restoring riparian forests and floodplain connectivity, correcting fish passage barriers, and reducing negative impacts of urbanization and forest clearing will provide significant benefits in terms of Chinook salmon viability,
particularly for spatial structure and diversity. Low flows are also thought to limit production in the Lower - Pilchuck sub-basin, and may also be a problem in other small rivers. Though recovery actions in this strategy group will not likely achieve as great an improvement in Chinook abundance and productivity as actions in the mainstem - primary restoration group, inactivity in the mainstem - secondary restoration areas probably will not allow the Snohomish River basin to reach recovery planning targets set by the co-managers.