We present a novel system of drifting pelagic baited stereo-video cameras that operate in deep-water, topographically complex environments typically considered inaccessible for sampling. The instruments are portable, semi-autonomous and inexpensive, allowing the recording of high-definition video footage in near-real time and over broad stretches of ocean space. We illustrate their benefits and potential as non-extractive monitoring tools for offshore marine reserves with a pilot study conducted within the newly established Perth Canyon Commonwealth Marine Reserve, southwestern Australia (32° S, 115° E). Using occupancy and maximum entropy models, we predict the distribution of midwater fishes and sharks and show that their most suitable habitat encompasses a wider fraction of the canyon head than is covered by park boundaries. Our proof-of-concept study demonstrates that drifting pelagic stereo-video cameras can serve as appropriate field platforms for the construction of species distribution models with implications for ocean zoning and conservation planning efforts.