We assessed changes in vegetative structure of 49 impoundments at Moosehorn National Wildlife Refuge (MNWR), Maine, USA, between the periods 1984–1985 to 2002 with a multivariate, adaptive approach that may be useful in a variety of wetland and other habitat management situations. We used Mahalanobis Distance (MD) analysis to classify the refuge's wetlands as poor or good waterbird habitat based on five variables: percent emergent vegetation, percent shrub, percent open water, relative richness of vegetative types, and an interspersion juxtaposition index that measures adjacency of vegetation patches. Mahalanobis Distance is a multivariate statistic that examines whether a particular data point is an outlier or a member of a data cluster while accounting for correlations among inputs. For each wetland, we used MD analysis to quantify a distance from a reference condition defined a priori by habitat conditions measured in MNWR wetlands used by waterbirds. Twenty-five wetlands declined in quality between the two periods, whereas 23 wetlands improved. We identified specific wetland characteristics that may be modified to improve habitat conditions for waterbirds. The MD analysis seems ideal for instituting an adaptive wetland management approach because metrics can be easily added or removed, ranges of target habitat conditions can be defined by field-collected data, and the analysis can identify priorities for single or multiple management objectives.