Reliable plans for desert bird conservation will depend on accurate prediction of habitat change effects on their distribution and abundance patterns. Predictive models can help highlight relationships between human-related and other environmental variables and the presence of desert bird species. Presence/absence of 30 desert bird species of Baja California peninsula was modelled on the basis of explanatory variables taken from the field, maps, and digital imagery. Generalized linear models were fit to each bird species using both variables representing human activity and other environmental factors as predictors that might influence distribution. Probability of species presence was used as a habitat suitability index to evaluate the effect of human activity when the model contained a significant human activity variable. No differences were found in bird species richness between natural sites and those transformed by agriculture or urbanization. Of 59 bird species recorded in surveys, 34% were positively or negatively associated with human-transformed habitats. Fourteen species seem to benefit from transformation of natural vegetation by agriculture or urbanization, while six were negatively affected. Sensitivity analyses of final models indicated all were robust. Results suggest that the occurrence of a large percentage of bird species inhabiting scrub habitats is sensitive to human habitat transformation. This finding has important conservation implications at regional scale as fragmentation and conversion of desert ecosystems into agricultural and urban areas affect the distribution of species that are highly selective for scrub habitat. Land use and anthropogenic activities seem to change ecological patterns at large spatial scales, but other factors could drive species richness distribution too (i.e. individual species response, species–energy relationships). The spatial modelling approach at regional scale used in this study can be useful for designing natural resource management plans in the Sonoran desert scrub.