There is an increasing interest in environmental DNA (eDNA) as a method to survey marine biota, enhancing traditional survey methods, and a need to ground truth eDNA-based interpretations with visual surveys to understand biases in both the eDNA and visual datasets. We designed and tested a rapidly-deployable, robust method pairing water sampling for eDNA collection and stereo-video imagery, comparing inferred fish assemblages with interspersed baited remote underwater video (stereo-BRUV) samples. The platform demonstration was conducted in proximity to a submerged ancient coastline feature in the no-take National Park Zone of the Ningaloo Marine Park, Western Australia. The system is capable of rapidly collecting simultaneous 270 degree stereo-video imagery, oceanographic measurements and multiple water samples across a range of habitat and depths (up to 600m). Combining simultaneous visual survey data with eDNA species estimates increased the total diversity of the fish assemblage by ca. 6.5% over eDNA estimates alone, whilst analysis of the assemblage composition sampled by each method revealed significant differences. The platform demonstration highlights the biases of each sampling method and their complementarity to one another. We suggest that these biases will be better understood by advancements that allow eDNA metabarcoding to discriminate the abundance and life-stage of marine biota. Furthermore, investigation of the relationship between eDNA metabarcoding data and concomitant imagery-derived length, age and habitat data is needed.