The diversity and abundance of wetland birds have been threatened by increasing anthropogenic activities during recent decades. The objective of this study was to determine the effect of human-induced disturbance on bird species richness and abundance of natural wetlands in southwest Ethiopia. Bird surveys were performed at 56 locations during both the wet and dry seasons in 2010 and 2011. Generalized linear modeling (G) was used to correlate species richness with environmental variables. It was found that wetlands with low human disturbance were characterized by a higher richness (n > 10) of wetland dependent specialist birds (depending completely on wetlands for food and nesting) than the highly disturbed wetlands. However, for wetland-associated birds (those able to nest and feed in wetlands as well as in other habitats), there was no significant difference (P = 0.31) in species richness between disturbed and non-disturbed wetlands. The abundance of wetland dependent specialist birds was significantly affected (P < 0.001) by human disturbance, whereas the abundance of wetland associated birds was not (P = 0.39). Fifty-three percent of the variation in species richness of wetland dependent birds was explained by a combination of water depth, sludge depth, conductivity, chlorophyll a, total phosphorus, human disturbance and vegetation cover. It is recommended that anthropogenic activities should be minimized and controlled in and around these wetlands to conserve biodiversity.