Similar to many large river valleys globally, the Sacramento River Valley has been extensively drained and leveed, hydrologically divorcing river channels from most floodplains. Today, the former floodplain is extensively managed for agriculture. Lack of access to inundated floodplains is recognized as a significant contributing factor in the decline of native Chinook Salmon (Oncorhynchus tshawytscha). We observed differences in salmon growth rate, invertebrate density, and carbon source in food webs from three aquatic habitat types—leveed river channels, perennial drainage canals in the floodplain, and agricultural floodplain wetlands. Over 23 days (17 February to 11 March, 2016) food web structure and juvenile Chinook Salmon growth rates were studied within the three aquatic habitat types. Zooplankton densities on the floodplain wetland were 53x more abundant, on average, than in the river. Juvenile Chinook Salmon raised on the floodplain wetland grew at 0.92 mm/day, 5x faster than fish raised in the adjacent river habitat (0.18 mm/day). Two aquatic-ecosystem modeling methods were used to partition the sources of carbon (detrital or photosynthetic) within the different habitats. Both modeling approaches found that carbon in the floodplain wetland food web was sourced primarily from detrital sources through heterotrophic pathways, while carbon in the river was primarily photosynthetic and sourced from in situ autotrophic production. Hydrologic conditions typifying the ephemerally inundated floodplain—shallower depths, warmer water, longer water residence times and predominantly detrital carbon sources compared to deeper, colder, swifter water and a predominantly algal-based carbon source in the adjacent river channel—appear to facilitate the dramatically higher rates of food web production observed in the floodplain. These results suggest that hydrologic patterns associated with seasonal flooding facilitate river food webs to access floodplain carbon sources that contribute to highly productive heterotrophic energy pathways important to the production of fisheries resources.

Tracking habitat use and dietary shifts in migratory species is vital to conservation and management. Yet, conventional animal tracking often precludes tracking small juveniles at critical life stages where recruitment bottlenecks often manifest. Stable isotope analysis (SIA) in consecutive laminae in eye lenses, a protein‐rich depositional tissue, has emerged as a promising tool in fishes to develop long‐term interpretive records of dietary histories using a single archival tissue. Currently, studies using fish eye lenses to study SIA in diets have primarily been conducted in marine environments using δ¹³C and δ¹⁵N to identify resource partitioning, ontogenetic shifts and lifelong trophic histories. To date, no studies have examined freshwater taxa nor used δ³⁴S isotopes. We placed juvenile (Chinook Salmon) Oncorhynchus tshawytscha in experimental enclosures in three different freshwater habitats (hatchery, river and seasonal floodplain), each with isotopically distinct and well‐characterized food webs. This experimental approach allowed us to directly measure diets and quantify tissue turnover rates in eye lenses as well as the isotopic fractionation among fish tissues (fin and muscle tissue) in distinct habitat types using stable isotopes δ¹³C, δ¹⁵N and δ³⁴S. Bulk eye‐lens stable isotope measurements were analysed for juvenile salmon lenses and were found to be consistent with the isotopic values of rearing habitats. Slight additional isotopic fractionation was only found in δ¹³C. We then successfully applied the method to a larger, reproductively mature adult salmon captured in freshwater and inferred juvenile habitat use. SIA in eye lenses using three dietary isotopes (δ¹³C, δ¹⁵N and δ³⁴S) has significant potential for answering critical questions about migration, diet, foraging ecology and life history of migratory aquatic animals on Earth. Such information would have immediate application towards conservation management of diverse species and habitats at multiple scales.

Coho salmon Oncorhynchus kisutch are a threatened species in California. In the Shasta River, they may be caught in an ecological trap that is exacerbating their decline. Adults appear to have equal preferences for spawning habitat that reduces the survival of their young and that of apparently similar quality where survival would be more likely. The primary cause of juvenile mortality is water withdrawals, which degrade summer water quality and create barriers to movement to habitats with more suitable rearing conditions. The situation has been exacerbated by the addition of gravel to support spawning fall‐run Chinook salmon O. tshawytscha, creating habitat that is also attractive to spawning coho salmon in locations where juvenile coho salmon survival will be extremely low. The Shasta River acts as a conceptual model of how habitat degradation and ecologically naive restoration actions may combine to create severe ecological traps for nontarget species. Received March 10, 2011; accepted October 11, 2011

In the Western United States, volcanic spring-fed rivers are anticipated to become increasingly more important for salmonids and other native fishes, as these rivers will retain coldwater habitats as the climate warms. Despite this, little is known about the hydro-biogeochemical interactions within these ecosystems. A review of existing literature on spring-fed rivers, coupled with a decade of research on volcanic spring-fed rivers of northern California, finds that these systems are exceptionally productive and exhibit stable environmental conditions. These unique conditions stem from hydrogeologic processes typical of young volcanic terrains. Aquatic macrophytes, common to some nutrient-rich spring-fed systems, play a disproportionate role in hydrologic and geomorphic processes by facilitating ecological interactions and velocity conditions that improve juvenile salmonid growth. We find that volcanic spring-fed rivers are also resilient to climate change, due not only to their ability to dampen water temperature changes through deep groundwater flow but also because of their nutrient-driven high ecosystem productivity, which may enable coldwater species to metabolically compensate for marginal increases in water temperature. Understanding the fundamental geomorphic and ecological differences between these rare ecosystems and their numerically dominant runoff rivers is essential for developing long-term conservation strategies for coldwater species under a rapidly changing climate.