The Flinders Commonwealth Marine Reserve (CMR) survey was a pilot study undertaken in August 2012 as part of the National Marine Biodiversity Hub's National monitoring evaluation and reporting theme. The aim of this theme is to develop a bluepint for the sustained monitoring of the South-east CMR Network. The particular aims of the survey were twofold; 1) to contribute to an inventory of demersal and epibenthic conservation values in the reserve and 2) to test methodologies and deployment strategies in order to inform future survey design efforts. Several gear types were deployed; including multibeam sonar, shallow-water (less than 150m) Baited Remote Underwater Video Systems (BRUVS), deep- water BRUVS (to 600 m), towed video and digital stereo stills. This resource contains the video and stereo still image data collected using a towed system (towed stereo camera system - TSCS). The TSCS was deployed using a probabalistic and spatially balanced survey design called Generalized Random Tessellation Stratified (GRTS). Habitats on the shelf were identified in a previous multibeam survey and consisted of 'mixed reef' (containing patchy reef) and sand. Mixed reef habitat was targeted in this survey (9 GRTS mixed reef sites versus 3 sand sites). Two roughly perpendicular TSCS tows were performed in each of those shelf GRTS sites. On the slope, down-slope (150-500 m depth) transect sites were classified by proportion of hard, soft and mixed bottom types based on multi-beam sonar (MBS) backscatter data. Transects with higher proportion of hard substrates were chosen using a GRTS approach. 7 transects were completed in the Flinders CMR, 5 transects in the adjacent Cape Barren Fisheries closure and two targeted transects were completed in a canyon to the north, where large coral bycatch had been reported from fisheries.