Quantitative, comparative studies are needed to better orient conservation efforts for the endemic, threatened avifauna of the Bogotá wetlands. The influence of landscape and local factors on abundance was studied for seven species: Bogotá Rail (Rallus semiplumbeus) and Apolinar's Wren (Cistothorus apolinari), endemic species; Ruddy Duck (Oxyura jamaicensis), Spot-flanked Gallinule (Gallinula melanops), American Coot (Fulica americana) and Yellow-hooded Blackbird (Chrysomus icterocephalus) with endemic subspecies; and the widespread Common Gallinule (Gallinula galeata). Areas, habitats and landscapes of nine urban and ten rural wetlands were quantified using GIS and remote sensor images; water quality and abundances of feral dogs and Shiny Cowbirds (Molothrus bonariensis) were evaluated in adjunct studies. Populations of focal species were estimated by point counts. Wetland variables were analyzed with principal component, canonical correlation and redundancy analyses and related to bird abundances and densities by multiple regressions. Most urban wetlands were covered by aquatic vegetation; rural wetlands were mostly open water with less vegetation. Abundances of all focal species increased with wetland area. Abundances of the endemic rail, wren and blackbird were correlated with emergent vegetation area and/ or negatively with open water, whereas duck, coot and gallinule abundances were correlated with open water area and/or negatively with urbanized landscapes, therefore both urban and rural wetlands are necessary for conservation of this endemic avifauna. Public investment has favored only some urban wetlands hence a regional, rather than local, approach to wetland management is needed. The situation of the wren is especially critical, probably due to brood parasitism by the cowbird.