Impact assessments are a valuable tool for investigating the effects of human-induced and natural perturbations on ecosystems and wildlife, including species of conservation concern. The breeding range of the golden-cheeked warbler (Setophaga chrysoparia), a federally endangered species, is located in a region with increasing development that includes housing, road construction and maintenance, and other land-use conversions; along with wildfire, oak wilt, and other disturbances. Although many of these actions are assumed to have deleterious effects on warbler occurrence or fitness, there is limited research directly investigating impacts of these activities to date. Many of these threats cannot be investigated within a fully manipulative study framework because it is rarely possible or even appropriate to replicate treatments. We conducted impact assessment studies investigating the effects of military training and highway construction on the warbler. We use these studies to provide examples that demonstrate how common challenges in investigating impacts can be addressed during planning and implementation by using alternative study design and sampling strategies to effectively assess the impact of perturbations on species of interest. © 2012 The Wildlife Society.