The upper third of the Hudson River has experienced thousands of hectares of shallow water habitat loss from filling shallow, low-velocity areas along the margins of the river with dredge material from channelization. Such low-velocity habitats often support high larval fish densities and serve as nursery habitat for many early life fishes. Moreover, the anadromous alewife populations along the Atlantic coast are in decline, including the Hudson River population. Early life is a defining stage in the life history of many fish species, with the relative abundance of populations being defined in the first few weeks of life. Therefore, the rehabilitation of previously filled nursery habitat for alewife and other Hudson River alosines could aid in the recovery of these species. This study considered larval fish presence in the context of different physiochemical parameters of shallow water microhabitats. Particular emphasis was placed on the distribution and ontogeny of larval alewife to inform habitat rehabilitation for this species. In order to sample in shallow areas as well as maintain the contrasts of intra-site variability, larvae were collected by random point abundance sampling using a throw trap within three shallow water sites in the Tivoli Bays Estuarine Research Reserve. Chapter 1 examined larval alewife distribution in relation to microhabitat structure using a logistic mixed effects model. Results indicated that alewives were more frequently present in lower velocity and deeper water while avoiding aquatic vegetation. Furthermore, larvae were caught more frequently during ebb tide and at low river water levels. These findings suggest that considerable local variation occurs within nursery habitat and that this variability affects habitat suitability. Chapter 2 examined the shift in habitat use and feeding of alewife over the larval period. Ontogenetic changes begin in the embryo and continue after hatching so that additional physiological and behavioral capabilities increase with age. A linear model was developed to explore the relationship between fish size and a variety of habitat and biological community metrics, including available habitat, degree-days, larval density, and feeding incidence. Furthermore, larval diets were examined to identify feeding shifts over larval ontogeny. Distinct shifts in habitat association and diet were found in feeding larvae. Larger fish were found at locations with deeper water and higher water velocity. Alewives fed on microzooplankton when first feeding and shifted to progressively larger prey organisms as they grow. The appendix characterized alewife habitat partitioning with the rest of the shallow water fish community using canonical correspondence analysis. Several differences in habitat use were found between and among larvae and adult fishes of the Tivoli Bays community. The most important environmental variables influencing the fish assemblage were depth, dissolved oxygen, distance from shore, substrate, temperature, and vegetation density (Trapa natans and Vallisneria americana). All groups of larvae and adults displayed unique environmental signatures, including the larval and mature tessellated darters (Percidae). The observed shifts in microhabitat association and prey choice for larval alewife and habitat partitioning of the fish community have implications for rehabilitating suitable nursery habitats. Both active orientations to structural habitat components as well as tidal transport mechanisms are suspected to influence intra-site distribution. Restoration plans targeting larval alewife should take into account this intra-habitat variation. Furthermore, rehabilitation should include micro-scale heterogeneity to accommodate the range of ontogenetic habitat associations of larval alewives as well as the early life history preferences of other target species.