Spatial structures of larval fish in the Strait of Georgia (British Columbia, Canada) were quantified in the springs of 2009 and 2010 to investigate linkages to environmental heterogeneity at multiple scales. By applying a multiscale approach, principal coordinate neighborhood matrices, spatial variability was decomposed into three predefined scale categories: broad scale (>40 km), medium scale (20∼40 km), and fine scale (<20 km). Spatial variations in larval density of the three dominant fish taxa with different early life histories (Pacific herring (Clupea pallasii), Pacific hake (Merluccius productus), and northern smoothtongue (Leuroglossus schmidti)) were mainly structured at broad and medium scales, with scale-dependent associations with environmental descriptors varying interannually and among species. Larval distributions in the central-southern Strait were mainly associated with salinity, temperature, and vertical stability of the top 50 m of the water column on the medium scale. Our results emphasize the critical role of local estuarine circulation, especially at medium spatial scale, in structuring hierarchical spatial distributions of fish larvae in the Strait of Georgia and suggest the role of fundamental differences in life-history traits in influencing the formation and maintenance of larval spatial structures.