While numerous studies have shown that floodplain habitat complexity can be important to fish ecology, few quantify how watershed-scale complexity influences productivity. This scale mismatch complicates population conservation and recovery strategies that evaluate recovery at regional or multi-basin scales. We used outputs from a habitat status and trends monitoring program for ten of Puget Sound’s large river systems to examine whether juvenile Chinook salmon productivity relates to watershed-scale habitat complexity. We derived habitat complexity metrics that quantified wood jam densities, side and braid to main channel ratios, and node densities from a remote sensing census of Puget Sound’s large river systems. Principal component analysis revealed that 91% of variance in these metrics could be explained by two principal components. These metrics revealed gradients in habitat complexity across Puget Sound which were sensitive to changes in complexity as a result of restoration actions in one watershed. Mixed effects models revealed that the second principle component term (PC2) describing habitat complexity was positively related to log transformed subyearling Chinook per spawner productivity rates from 6–18 cohorts per watershed. Total subyearling productivity (subyearlings per spawner) and fry productivity (subyearling fry per spawner) rates were best described by models that included a positive effect of habitat complexity (PC2) and negative relationships with log transformed peak flow recurrence interval, suggestive of reduced survival due to egg destruction during floods. Total subyearling productivity (subyearlings per spawner) and parr productivity (subyearling parr per spawner) rates were best described by models that included a positive effect of habitat complexity (PC2) and negative relationships with log transformed spawner density, suggestive of density dependent limits on juvenile rearing habitat. We also found that coefficient of variation for log transformed subyearling productivity and subyearling fry productivity rates declined with increasing habitat complexity, supporting the idea that habitat complexity buffers populations from annual variation in environmental conditions. Therefore, we conclude that our watershed-scale census-based approach provided habitat complexity metrics that explained some of the variability in productivity of subyearling juveniles among Chinook salmon populations. Furthermore, this approach may provide a useful means to track and evaluate aggregate effects of habitat changes on the productivity of Endangered Species Act (ESA) listed Chinook salmon populations over time.

In this paper, we use a system‐wide census of large river and floodplain habitat features to evaluate influences of valley form and land use on salmon habitats along 2,237 km of river in the Puget Sound region of Washington State, USA. We classified the study area by geomorphic process domains to examine differences in natural potential to form floodplain habitats among valley types, and by dominant land cover to examine land use influences on habitat abundance and complexity. We evaluated differences in aquatic habitat among strata in terms of metrics that quantify the length of main channels, side channels, braid channels, and area of wood jams. Among geomorphic process domains, habitat metrics standardized by main channel length were lowest in canyons where there is limited channel migration and less potential to create side channels or braids, and highest in post‐glacial and mountain valleys where island‐braided channels tend to form. Habitat complexity was lower in glacial valleys (generally meandering channels) than in post‐glacial valleys. Habitat abundance and complexity decreased with increasing degree of human influence, with all metrics being highest in areas classified as forested and lowest in areas classified as developed. Using multiple‐year aerial photography, we assessed the ability of our methods to measure habitat changes through time in the Cedar and Elwha Rivers, both of which have recent habitat restoration activity. We were able to parse out sources of habitat improvement or degradation through time, including natural processes, restoration, or development. Our investigation indicates that aerial photography can be an effective and practical method for regional monitoring of status and trends in numerous habitats.