LAUSR

Abstract The role that west coast estuarine habitats play in the early life history of many nearshore marine fishes is poorly understood, in part due to the limited temporal sampling of estuarine habitats. To begin to understand this role, we compared the juvenile demersal fish community between two habitat types at a marine-dominated estuary on the northeast Pacific coast and examined how community structure changed temporally. Sampling occurred in Yaquina Bay, Oregon during 2008–2009, 2012–2013, and 2016–2017 at eleven sites, comprised of anthropogenic (dock) and natural (eelgrass) habitats. The juvenile fish assemblage was dominated by a few highly abundant species, including saddleback gunnel (Pholis ornata), Pacific staghorn sculpin (Leptocottus armatus), and rockfishes (Sebastes spp.), with the majority of species being marine associated. Community structure varied among years and between habitat types, with greater differences seen between habitat types than years. Docks appear to be a specialized habitat, supporting some species but with greater change in community structure over time and lower overall abundances than eelgrass. Use of docks by commercially and recreationally-exploited species, though, indicates potential importance. Community structure differences were best described by a combination of regional (Pacific Decadal Oscillation) and local (upwelling, temperature, salinity) climate variables, but correlation values are considered weak. Greater abundances and reduced change in communities over time at eelgrass sites suggests that maintaining these habitats is potentially critical for many estuary-rearing species, and temporal changes in these communities highlight the importance of long-term monitoring.