Atlantic menhaden (Brevoortia tyrannus) is well-known for its commercial and ecological importance and has been historically declining in the Chesapeake Bay, Maryland, one of its principal nursery habitats along the eastern coast. Utilizing data from the Striped Bass Seine Survey of the Maryland Department of Natural Resources, we evaluated how the distribution of over 1 million Atlantic menhaden had changed from 1966 to 2004 for 12 river drainages. We observed significant or marginally significant declines in 42% of the drainages, with drainages of the northern Bay showing the majority of those declines. Continued recruitment to several drainages of the Bay may partly explain why the adult spawning population is not putatively declining. We determined if temporal changes in abundance were related to changes in salinity or water quality for five major drainages of the watershed. For one of these drainages, the Patuxent River, differences in productivity across sites largely explained differences in abundance. For the four remaining drainages, differences in recruitment could not be explained by salinity or productivity. During 2005 (July-August), we sampled four rivers of the Chesapeake Bay watershed and two rivers of the Delaware Bay watershed to compare habitat use by recruiting Atlantic menhaden. We collected 69 juvenile Atlantic menhaden, which were most abundant in the Choptank River. Abundance was highest downstream for rivers of the Delaware Bay, suggesting a distributional relationship to salinity. In the four rivers of the Chesapeake Bay, preliminary data indicate a weak relationship of Atlantic menhaden to land use, salinity, or other physical factors and on-going work will elucidate the relationship between phytoplankton size and community structure to the distribution of Atlantic menhaden. While reducing nitrogen loading and enhancing water clarity may improve Atlantic menhaden production, we suggest that the role of offshore processes on large-scale declines has been largely neglected and studies on larval ingression are necessary for further elucidation of spatial and temporal patterns of juvenile distribution in the Chesapeake Bay.