Freshwater habitat

High levels of mercury and other toxic chemicals are showing up in seemingly remote and pristine parts of the Puget Sound watershed, the result of atmospheric deposition. Scientists talk about a “dome” of pollution hanging over urban areas, leading to a never-ending cycle of persistent compounds working their way through the air, onto the land and into the water.

The watersheds of Washington’s San Juan Islands were thought to be too small to support wild salmonid populations, and many streams flow only seasonally. But a 2019 article in the journal Conservation Genetics reports that at least five watersheds in the region support populations of coastal cutthroat trout (Oncorhynchus clarki clarki). Genetic analysis of the cutthroat trout in three of the watersheds suggest two support native populations. The findings are important for understanding the conservation status of these previously unknown populations. 

Spring and fall Chinook salmon were thought to be alike until researchers discovered a gene for early migration. Now, federal biologists and legal experts are struggling to decide if spring Chinook should be granted their own legal protection under the Endangered Species Act.

Freshwater habitat in the Puget Sound region consists of rivers, marshes, streams, lakes and ponds that do not have any saltwater input. Many species depend on these freshwater resources, including salmon, salamanders, frogs, and beavers.

Eight aquatic reserves, managed by the Washington Department of Natural Resources, have been established to protect important ecosystems on state aquatic lands.

In most reserves, area residents work with state, local and tribal officials and nonprofit groups to develop and carry out management plans, including scientific research.

The aquatic reserves in the order they were established include: 

• Maury Island 2004
• Cypress Island  2007
• Fidalgo Bay 2008
• Cherry Point 2010
• Protection Island 2010
• Smith and Minor Islands 2010
• Nisqually Reach 2011
• Lake Kapowsin 2016

The Puget Sound River History Project at the University of Washington features historical topographic data for Puget Sound's river systems.