The impacts of fishing within the Ningaloo Marine Park can be estimated by comparing sites inside and outside no-take sanctuary zones and sites across a gradient in recreational fishing pressure. We present data from baited remote underwater stereo-video (stereo-BRUV) and diver operated stereo-video (stereo-DOV) to estimate variation in the abundance distribution of fish and shark species and habitat composition across the region. We find that habitat composition, in particular the complexity of relief, to be a strong predictor of fish and shark assemblages sampled by stereo-BRUV and stereo-DOV. Only from stereo-BRUV data, we also found evidence of protection from fishing within no-take sanctuary zones for fish species and for shark species we found evidence of impacts of fishing where intensity of recreational fishing pressure was greatest. We suggest the differences in results from baited video and dvier video survey methodologies may be due to fish behaviour.