Disruption of natural disturbance regime decouples habitat and life stage in a keystone species

Abstract Anthropogenic disturbance of stream ecosystems, often chronic in nature, has been studied extensively. However, when disturbance is driven by more than one resource policy over many decades, feedback between habitat evolution and biological adaptation can be disrupted and ecological function affected in unforeseen ways. We analyzed over 100 years of Chinook salmon ( Oncorhynchus tshawytscha ) length frequency trends associated with fisheries management and changes in available spawning substrate (habitat) linked to flow regulation in a highly altered California river. Over time, salmon lengths generally decreased, fluctuating with exploitation (ocean harvest) and hatchery production rates. Female size reduction, coupled with a degrading and coarsening channel, and perching peripheral habitat related to past mining activity, indicates available spawning substrate may be too large to support the current salmon population. Assuming a salmon can move material ~10% of her body length, length frequency data and current substrate size distribution suggest that increasing salmon sizes to historic distributions could increase available spawning habitat by as much as 13%. Alternatively, decreasing spawning substrate size could support a greater portion of the current population. To test the latter hypothesis and inform future management actions, we monitored two spawning riffles where large and small gravel was placed on top of a cobble. We observed an immediate spawning activity increase that was more pronounced where smaller gravel was deposited. Following a decade of habitat decline, the two sites were both replenished with medium gravel. Elevated spawning use occurred immediately at both sites, commensurate with this intermediate size, further supporting our hypotheses. Sediment coarsening and habitat disconnect below dams, combined with reduced salmon size, indicate the natural spawning process may be decoupled from available habitat below dams in the foreseeable future without continuous intervention. Actively managing salmon population demographics through modified hatchery and size‐selective harvest practices and developing a coarse sediment budget with size‐appropriate material for regulated anadromous rivers could produce immediate benefits for ecosystem services, including salmon populations. However, these management actions will require continued maintenance and informed socio‐ecological goals to remain successful.