Habitat degradation leads to homogenization of biological communities, often due to the dominance of generalist species over specialists. Yet data as to how life history attributes of specialists vary with such perturbations remain sparse. We compared long-term population dynamics of a specialist trawling bat, the large-footed myotis (Myotis macropus), between two forested catchments. One forest stream was nutrient-enriched from dairy farming in its headwaters and a portion of its surrounding catchment was harvested for timber during the study, while the other was located in primarily undisturbed forest. We caught and banded bats annually at their roosts over 14 years and banded 529 individuals with a 45% recapture rate. The maximum time to recapture was nine years and there was no evidence for transiency in our populations. Mark-recapture analyses allowed for investigation of the dependence of survival on time, sex, and age at marking. Our study spanned extreme El Niño and La Niña weather events, but we found little variation in survival, although recruitment was lower during drought. Mean minimum winter temperature (positive) and rainfall (positive) had weak influences on survival. Survival of adults (∼0.70) and population size of adult females was similar between the two sites, suggesting that neither timber harvesting with retained riparian buffers nor eutrophication from farming influenced survival. Survival of adult males and females was similar, but survival of juveniles was less than half that of adults, probably due to a combination of mortality and dispersal. Survival was three times lower immediately after one of the timber bridges used as a roost fully collapsed. Specializing on aquatic habitats buffered M. macropus from most extreme weather, but there was also evidence for possible mortality and recovery after an intense rainfall and flooding event immediately prior to the study. More frequent intense rainfall predicted with global warming may reduce the species' resilience over time.