Many migratory shorebirds rely on estuaries as stop-over sites to refuel during migration, and the loss of stop-over sites is a primary threat to shorebird populations on the West Coast of the United States (e.g. Calidris alpina pacifica, C. mauri). Conservation and research has focused on the largest of these sites; however, smaller estuaries also host thousands of migratory shorebirds. Furthermore, the reasons for site selection are largely unknown. Estuarine inter-tidal microhabitats are non-uniform and both abiotic and biotic factors may serve as predictors of whether an abundance of shorebirds will use a site. I investigated shorebird site selection on broad and fine scales within Oregon estuaries. To identify factors that relate to shorebird abundance on large spatial scales, I compiled shorebird abundance data from estuaries throughout the Pacific Northwest as well as data on site quality factors. To investigate site selection on a finer scale I measured shorebird abundance, habitat characteristics, and food resources―invertebrates and a newly considered source, biofilm―within two Oregon estuaries during the fall migration period. Finally, I examined whether channels are preferentially used by foraging Calidrid shorebirds by conducting observations during the spring migration. I investigated whether channels may be superior foraging habitat possibly because prey are more abundant, are found at shallower depths, or because sediments are more penetrable (increasing the opportunity for shorebird probing) by taking infauna cores and measuring force required to probe in the sediment at channel and open mudflat sites. Among estuaries, shorebird densities in spring were best predicted by estuary size, as opposed to the amount of any one habitat. During fall migration, the amount of grassland in the surrounding watershed was also a good predictor, pointing to the probable importance of roost sites as well as feeding grounds. The amount of infauna also related to the density of shorebirds using a site. Within estuaries, shorebird distribution in the inter-tidal region was not generally predicted by prey abundance. Channels were used preferentially by shorebirds, and infauna abundance along channels was greater than in the surrounding mudflats. The more penetrable sediments of the channel also made it easier for shorebirds to probe and capture prey. Identification of these large-scale and fine-scale factors that influence site quality for migratory shorebirds will assist land and wildlife managers' efforts to protect these species.