Some oil spills cause losses of ecological services in coastal wetlands, other shoreline environments, intertidal ecosystems, and upland environments. In the United States, habitat equivalency analysis (HEA) is being used frequently in natural resource damage assessments for such oil spills to determine the scale of compensatory-restoration projects needed to offset the ecological service losses. The cost of the scaled compensatory-restoration project(s) that offset the ecological service losses is the measure of natural resource damages for the lost ecological services. Our paper describes the HEA process and provides an example of its application. Then we examine several challenges that arise in some HEA applications, including the role of leasing versus purchasing compensatory habitat, increasing values of compensatory habitat over time due to decreasing availability, accounting for service gains from compensatory habitat in the distant future when the present value of those services is essentially zero, and addressing uncertainties in estimating HEA inputs (such as the magnitude of annual service losses and gains). The final section of our paper provides our conclusions with respect to these challenges.