Habitat quality was assessed for two native osmerids, delta smelt Hypomesus transpacificus and longfin smelt Spirinchus thaleichthys, between two distinct nursery areas located in the low-salinity zone of the San Francisco estuary. The relationship between several variables was investigated including fish density, fish size, feeding success and the general condition of larvae as well as juveniles for both species. The nursery habitats that were evaluated included the North and South Channels of Suisun Bay. The results showed higher densities of zooplankton and decreased water velocities for the North Channel when compared to the South Channel. The dominant prey item was calanoid copepod Pseudodiaptomus forbesi for both species although longfin smelt residing in the North Channel also included another copepod in their diets, Acanthocyclops spp. In both locations, delta smelt fed predominantly during daytime flood tides, while longfin smelt feeding appeared to continue into the night hours. When both locations were compared, delta smelt in the North Channel exhibited higher densities, larger sizes, increased somatic condition and larvae <15 mm standard length demonstrated greater feeding success. Longfin smelt, exhibited similar densities, feeding success and size distributions between both channels, but generally showed poorer somatic condition for the South Channel, potentially due to energetic costs associated with documented vertical migration behaviour. Overall, the physical conditions of the North Channel provided superior habitat for both species, while the South Channel afforded only marginal habitat for longfin smelt and very poor habitat for delta smelt. Therefore, the North Channel of Suisun Bay acts as critical nursery habitat by providing better feeding and growing conditions leading to increased health and survival for both species.