We sampled blood from free-living spotted salamanders (Ambystoma maculatum) to test whether differences in the concentrations of a stress hormone (corticosterone) were associated with different qualities of breeding and migration habitat. Spotted salamanders are forest specialists that migrate to vernal pools to breed, and upland habitat degradation may have sub-lethal effects on animals that lead to population declines. An individual's level of physiological stress may function as a biomonitor for sub-lethal effects, and thus as a biomonitor for ecosystem quality. We compared unstressed (baseline) and stress-induced corticosterone concentrations in spotted salamanders: (1) at sites that differed in amount of forest loss; (2) during breeding migration across forest habitat versus pavement; (3) in microhabitats that varied in soil drainage and canopy cover. Removal of large amounts of terrestrial habitat surrounding a breeding pond was correlated with lower baseline (in males) and stress-induced corticosterone concentrations, which may indicate healthy individuals with a reduced ability to respond to additional stress or individuals experiencing chronic stress. Male salamanders migrating across pavement had elevated baseline corticosterone concentrations compared to animals migrating through a forest, consistent with an acute stress response. However, concentrations of corticosterone did not differ between individuals in microhabitats with canopy cover and well-drained soil versus those in microhabitats with no canopy cover and/or swampy soil. This endocrinological technique may be one useful measure of a population's health, helping to identify populations where further ecological study is recommended to evaluate conservation concerns.