Geographically-based threat assessments are important for identifying natural resources at risk, yet have rarely been applied to identify habitat conservation priorities for imperiled organisms at a local scale. Pool-breeding amphibians have complex life cycles that place them at risk from habitat loss and fragmentation both in wetlands and in adjacent uplands. Because the most rapidly growing cause of habitat degradation in North America has been urbanization, a threat analysis of pool-breeding amphibian habitat should both be dynamic, i.e., sensitive to land-use change, and comprehensive, recognizing traditional protected area networks as well as less formal conservation assets (e.g., land-use regulations). To assess threats to wood frogs (Rana sylvatica) and spotted salamanders (Ambystoma maculatum) in a rapidly urbanizing, forested region of New England (USA) we examined gaps in the current protection network, as well as changing human settlement patterns. We found that greater than 50% of 542 potential breeding pools delineated using low-level infra-red aerial photography (median area 379.5 m2) were not represented on National Wetland Inventory (U.S.FWS) maps, and thus de facto at risk. Most importantly, conservation lands and regulatory protections failed to protect 46% of potential breeding pools and 80% of adjacent non-breeding habitat. While an assessment of human settlement patterns projected that only 5% of the region contained high quality amphibian habitat under acute development pressure, nearly half of the region (44.7%) had attained a moderate threat level, highlighting the importance of conservation planning during early stages of urbanization. We conclude by illustrating the role for multiple conservation strategies when protecting functional landscapes for pool-breeding amphibians.