The roosting ecology of most waterbird species is poorly known and even less is known from southern Asia, where many species inhabit human-modified areas. Roosting ecology of the Black-headed Ibis (Threskiornis melanocephalus) was studied in urban and rural settings in southern Rajasthan, India. Analyses focused on assessing whether site characteristics varied between nest sites, urban and rural roost sites, and paired sites (i.e., a waterbird roost site near Black-headed Ibis roosts but without Black-headed Ibis). Additionally, the hypothesis that factors affecting Black-headed Ibis numbers at roosts would be similar at urban and rural sites was tested. Tree characteristics (canopy cover, girth at breast height) were different (P < 0.05) between nest and roost sites. Urban roost sites experienced 2.3 times greater disturbance than rural roost sites. Paired site characteristics were similar to urban roost sites (multi response permutation procedure, significance of δ = 0.3), but were dissimilar to rural roost sites. Co-occurring roosting bird assemblages were significantly different between roosts and paired sites (significance of δ < 0.01) in urban and rural settings. Black-headed Ibis numbers at urban roosts were influenced by multiple variables, but models showed considerable ambiguity at rural sites. Results strongly suggest that including roost sites in a species status assessment is important.