Quantifying Abiotic Habitat Characteristics to Determine Thresholds for Salmonid over-Summer Survival in Intermittent Streams

We conducted repeat surveys of juvenile salmonid (Oncoryncus mykiss and O. kisutch) abundance, water temperature, DO concentrations, water depth and velocity, pool volume, and organic carbon concentrations and quality on two tributaries of Salmon Creek (Sonoma Co., CA, USA). We instrumented study reaches with piezometers containing thermistor arrays, which we use to calculate vertical groundwater flux, and installed one continuous water quality sonde. We used a hierarchical modeling framework to assess the survival of stream fish from paired sampling of discrete habitat units and investigated the relative importance of flow, fragmentation, and habitat quality to fish over-summer survival. Results indicate that dissolved oxygen drops to critical levels in many isolated pools, and the most parsimonious models included June count, maximum conductivity,  minimum DO, and density x DO interactions. We found high survival in some isolated pools that contained groundwater seeps, larger volume, and large woody debris or other cover. Our results demonstrate the importance increasing of late-season groundwater flow to benefit juvenile salmonids, and suggest that salmonid recovery and stream restoration strategies should target “sanctuary reaches” that possess adequate flow and structural complexity to support summer rearing.