The Yukon-Kuskokwim Delta of Alaska is a globally important region for numerous avian species including millions of migrating and nesting waterbirds. Climate change effects such as sea level rise and increased storm frequency and intensity have the potential to impact waterbird populations and breeding habitat in the near future. In order to determine the potential impacts of these climate-mediated changes, it is important to monitor the current spatial distribution of important nesting areas and understand the importance of environmental variables in the selection of nest locations. To do this, we modeled nest density for 15 species or composite species of waterbirds that commonly breed on the Yukon-Kuskokwim Delta, including Cackling Goose (Branta hutchinsii minima), Emperor Goose (Chen canagica), Black Brant (Branta bernicla nigricans), Greater White-fronted Goose (Anser albifrons frontalis), Tundra Swan (Cygnus columbianus), Sandhill Crane (Grus canadensis), Spectacled Eider (Somateria fischeri), Common Eider (S. mollissima), Northern Pintail (Anas acuta), Greater Scaup (Aythya marila), Pacific (Gavia pacifica) and Red-throated Loon (G. stellata; composited into one classification due to inability to distinguish nests), Glaucous Gull (Larus hyperboreus), Mew Gull (L. canus), Sabine’s Gull (Xema sabini), and Arctic Tern (Sterna paradisaea). The data used were from single-visit nest searches on 2,338 plots sampled during 29 years, 1985–2013. Nest density was modeled for each species using negative binomial regression and landscape environmental variables. For most species, nest density was greatest near the coast and within lower coastal salt marsh and upper coastal brackish meadow habitats. When compared to a withheld portion of the data, predicted nest densities were highly correlated (i.e., Spearman’s rank correlation coefficient, rs = 0.52–0.77) for 6 of the 15 species, but less correlated (rs = 0.24–0.49) for the remaining 9 species. Predicted nest densities mapped across the coastal zone of Yukon-Kuskokwim Delta for each species revealed areas of high and low densities that can be used to inform management and conservation decisions.