We studied the relationships between the habitat use of migratory shorebirds and the spatial distributions of the Southwestern Atlantic Fiddler Crab Uca uruguayensis, polychaetes, sediment characteristics and tidal levels in the Río de La Plata estuary, Argentina, where U. uruguayensis is one of the most important intertidal species. Crabs have a well-defined patchy distribution that is segregated spatially from that of polychaetes. Crab density on the surface varied across the tidal cycle, reaching maximum values during low tide. Polychaete density decreased with depth but showed no change through the tidal cycle; however, given that sediment penetrability did change during the same period, their availability to probing shorebirds is expected to change. Habitat use by shorebirds followed the spatial distribution of prey; shorebirds that foraged on polychaetes (White-rumped Sandpiper Calidris fuscicollis, Two-banded Plover Charadrius falklandicus and Hudsonian Godwit Limosa haemastica) focused their attention on the areas with the highest densities of polychaetes, whereas species that preyed mostly on crabs (Ruddy Turnstone Arenaria interpres, Whimbrel Numenius phaeopus and Grey Plover Pluvialis squatarola) predominantly used areas with crabs. This segregation occurred particularly during low tide, a period in which polychaetes became fully available. Results show that the spatial and temporal heterogeneity of mudflats in relation to the types and availability of prey has a strong effect on shorebird habitat use.