Populations occupying isolated aquatic habitats may be susceptible to local extinction following natural environmental fluctuations.  Inherent conservation concern increases with increasing human-induced environmental impact.  We propose that conservation effort be focused on a subset of populations with the strongest evolutionary potential to persist through change.  The flightless giant water bug Abedus herberti occupies isolated mountain headwater streams throughout the Madrean Sky Islands region of Arizona/Sonora.  Local populations show both divergent adaptive traits and strong population genetic differences.  These headwater habitats are of imminent conservation concern under climate change projections of increasing drought, which recently has caused drying of some streams followed by local extinctions of Abedus and other drought-intolerant species.  Here, we develop a composite metric to infer recent local population demographic stability from a suite of six statistics based on various properties of the haplotype distribution.  Results can be interpreted along a continuum from severe bottleneck to long-term stable growth.  For 16 populations , we demonstrate that this composite value is significantly correlated with dry-season wetted habitat area, a variable that likely reveals information about the natural probability of drying and subsequent population bottleneck or extinction.  This approach has strong potential for prioritizing local populations for conservation effort.