Climatic flux together with anthropogenic changes in land use and land cover pose major threats to wildlife, but our understanding of their combined impacts is limited. In arid southwestern North America, ferruginous pygmy-owls (Glaucidium brasilianum) are of major conservation concern due to marked declines in abundance linked to changes in land use and land cover during the past century. We reassessed abundance trends of pygmy-owls in northern Mexico across 17 years (2000-2016), which included data gathered over four additional years since inferences were last reported. We also assessed spatiotemporal trends in territory occupancy (n = 151 territories) across a much larger area that spanned 14 watershed regions in northern Mexico and adjacent Arizona over 16 years (2001-2016). Finally, we evaluated the influence of temperature, precipitation, land-use and land-cover change, spatial variation in local habitat quality, and interactions among these factors on occupancy dynamics. Large increases in abundance in 2015 and 2016 eliminated evidence of population declines that was described recently (e.g., Flesch 2014a) based on two modeling approaches. Moreover, there was little evidence of systematic temporal declines in territory occupancy across the broader bi-national study area, or for population units in Mexico and the adjacent U.S. Instead, occupancy dynamics varied at smaller spatial scales among watershed regions. We found that subpopulations in six regions declined or marginally declined across time, including two in the U.S. that declined to extinction; subpopulations in six other regions were stable; and those in two regions increased or marginally increased. Although variation in territory occupancy was associated with changes in temperature, precipitation, anthropogenic disturbance, and local differences in habitat quality, evidence for interactions among these factors was much greater than that for additive relationships. Territory occupancy declined with rising minimum air temperatures during winter at a much greater rate in disturbed landscapes compared to those with little to no anthropogenic disturbance. Moreover, occupancy increased with annual precipitation at increasingly positive rates as local territory quality increased. Such results suggest a complex set of processes simultaneously drove changes in territory occupancy, likely by influencing food abundance and the quantity, connectivity, and quality of habitat. Management focused on 1) protecting high-quality habitat, 2) enhancing and creating habitat (e.g., nest-cavity augmentation, riparian restoration), 3) reducing deleterious changes in land use and land cover, and 4) increasing landscape connectivity through both passive (e.g., landscape planning and restoration) and active (e.g., facilitated dispersal, translocations) techniques will enhance recovery prospects for pygmy-owls.