The freshwater life cycle of salmonids have evolved for diverse habitats created by diverse geophysical processes and climate. In California, there are three main geophysical/climatic zones. Each of the three zones: the Coast Ranges, the Sierra Nevada Mountain Range, and the huge tectonic valleys, which will not be discussed in detail, have unique habitat suiting different salmonid life history strategies. Climate is a key driver of watershed processes. California is 800 miles long (north to south) with a characteristic Mediterranean climate overlain by the El Niño Southern Oscillation climate cycle. These general weather patterns result in one wet winter per five year period and little to no precipitation in summer in the south and central coast areas giving way to a more annual cycle in the north coast area where El Niño and La Niña overlap. California is characterized by tectonically active and relatively young and erodible geologic formations. The Coast Range, in particular south of Monterey Bay, are vegetated by Chaparral shrubs that undergo cycles of the wildlife followed by flow and sediment events. These processes, combined with the El Niño Southern Oscillation climate cycle, result in some of the most dynamic and highest sediment yielding watersheds documented, and unique flow and sediment regimes for every watershed. The Sierra Nevada Mountains receive most of their precipitation as snow, which has a prolonged melt period and flow regime, and those watersheds are relatively moderated in physical processes and habitat reliability.
The two foundational components of freshwater salmonid habitat, land and water are today significantly compromised in California. A few decades of wild gold mining in the Sierra Nevada Mountains and some Coastal streams, followed by two centuries of land water development have taken a toll on most of the salmonid habitat in California. Gold bearing gravel deposits were dredged and hydraulically mined in many Sierra and some Coast Range streams, disturbing habitat and leaving uninhabitable waster piles. Low lying alluvial basins, where wetlands and wandering streams occurred, were dramatically altered to optimize arable land and drained to expedite runoff. In the Sierra Nevada Mountains, dams are found in all but one watershed, all major alluvial valleys and wetlands have been drained, diked, and remnant wetlands isolated from streams. This area is characterized by flood control and land expansion projects leading to stream encroachment and stream simplification into straight, incised, re-vetted, and channels subject to flash flooding, where sediment resources are unnaturally and frequently mobile and habitat is depleted. Significant effort has been expended to improve compromised channels by removing passage barriers at road crossings, and adding cover and structure to the streams to increase complexity.
Scientists have only recently found that salmonid growth and population abundance are regulated by wetland food resources. Indeed the persistent steelhead populations are found downstream from dams in 'tailwater' habitats, and the last wild coho salmon populations are found in watersheds where functioning wetlands persist (e.g. Green Valley Creek and the Atascadero wetland complex). Historic reconstructions of freshwater habitats document that wetlands and vast seasonal floodplains were common valley landscapes prior to Anglo development.
Recognizing the importance of freshwater habitat, the Pacific Fishery Management Council has identified five HAPCs for Pacific Coast salmon, including complex channels and floodplain habitats, thermal refugia, and spawning habitat. Estuaries, and marine and estuarine SAV are also designated as HAPC. See Appendix A of the Pacific Coast Salmon Fishery Management Plan for a description of the HAPCs.
