In arid zones, riparian corridors serve as important habitats, offering water, nutrients, shelter and optimal microclimate conditions to many organisms. In the northern Negev desert of Israel, several large rivers cross through the arid landscape, with Saltcedar (Tamarix spp.) being the climax vegetation. Although these rivers have been continuously subjected to management, human control became much more frequent and thorough since the early 2000s. Current management involves vegetation clear-cutting of long riverbed sections. In arid zones such as the Negev, where trees are scarce and restricted to streams, such activity may affect wildlife at all hierarchical levels. Being one of the most successful invasive trees in North America, many aspects of Saltcedar management along rivers have been explored around the USA. Notably, how riparian Saltcedar forests in the old world, where it is native, influence wildlife, has not been studied. We explored the effects of vegetation clear-cutting on bird communities at three sites in the Northern Negev of Israel, comparing bird abundance, richness and diversity between natural and managed riparian transects. All three variables were significantly lower in managed sites. Species composition shifted from tree-dwelling species in natural transects to ground-dwelling species in clear-cut sections. Natural sections were characterized by lower ambient temperature, lower radiation, and higher relative humidity. Our findings may explain the long-term reduction observed in local bird populations in the northern Negev. They also indicate the importance of the Saltcedar forests along major watersheds in the Northern Negev for bird populations.