Top-down (i.e., predation), bottom-up (i.e., food availability), and physical factors may influence blue crab (Callinectes sapidus) distribution. To assess the role of bottom-up and physical process in blue crab distributions, we concurrently measured density of the blue crab (Callinectes sapidus), density of its principal prey, the Baltic clam (Macoma balthica), and physical characteristics in mud and sand habitats spanning various spatial scales (1-10 km and 10-50 km) in the York River, Chesapeake Bay. Clam and crab densities were intermediate in mud, low in downriver sand, and high in upriver sand. Clam and crab densities were not correlated in mud. whereas in sand, they were significantly and positively correlated at both the local scale (I km) and at the broadest spatial scale (10-50 km). Crab density also correlated with salinity at the broad spatial scale. After removing the effect of salinity, crab density remained significantly correlated with clam density. Using a hydrodynamic model for the York River, potential transport of clams from downriver coves was primarily to upriver habitats, but transport of crabs was mainly to downriver seagrass habitats. At the local scale, upriver zones where crab and clams were abundant, crab density was highly correlated (r(2) = 0.93) with clam density, but not with salinity, suggesting that the distribution of blue crabs was driven mostly by their primary food item-clams. The collective findings are consistent with the hypotheses that crab density is driven by both food availability and salinity at broad spatial scales (10-50 km), whereas food availability is a primary control at smaller spatial scales (1-10 km). Bottom-up control of upper trophic levels may be distinctive; thus far, in marine and freshwater systems, bottom-up control has not been demonstrated to filter from basal to upper trophic levels. Furthermore, unvegetated habitats where food, such as clams, is abundant may be important in the population dynamics of the blue crab, even in systems where seagrass beds are common.