Unlike many other taxa, for bats base-line data to identify changes in status is virtually non-existent. We present mark-recapture analyses (17 years) targeting a habitat specialist, the large-footed myotis Myotis macropus, on two streams in northern NSW with contrasting disturbance history. We caught bats annually and banded 529 with a 50% retrap rate. The maximum time to recapture was nine years. Analyses allowed for dependence of survival on time, sex, and age at marking. Bats had a higher probability of recapture at the logged site (mean adult female = 0.74) compared with the undisturbed site (mean adult female = 0.33) and there was no evidence for transiency. Adult survival showed only minor fluctuations over time, suggesting that logging did not influence survival. Adult female survival averaged 0.74 ± 0.01 in the undisturbed site compared to 0.70 ± 0.003 in the seven years post-logging at the second site. Adult female population size was similar between the two sites. Our study spanned extreme El Nino and La Nina events, yet we found little variation in survival. There was some support for a minor influence of winter temperature (+ve) and rainfall (+ve) on survival. Adult male and female survival was similar at the logged site, but juvenile survival was less than half that of adults, probably because of mortality and dispersal. Our results suggest that riparian buffers retained during logging operations mitigate potential impacts on stream habitat for M. macropus and that specialising on aquatic habitats buffers the species from extreme weather.