Seagrass habitats worldwide are degrading and becoming fragmented, threatening the important ecosystem services they provide. Fauna associated with seagrasses, particularly cryptic species, are expected to respond to these changes, but are difficult to detect at ecologically meaningful scales using non-extractive techniques. We used a small, wide-angle camera (GoPro) and a small quantity of bait positioned within the canopy of Posidonia australis meadows in Jervis Bay, New South Wales to assess the response of fishes to seagrass cover. We saw a clear positive relationship with the condition of P. australis; a high cover of this seagrass had positive effects on the diversity and abundance of cryptic fauna. Our findings highlight ecosystem shifts associated with the loss and fragmentation of biogenic habitat. These changes are of particular relevance for P. australis meadows given their current status as an endangered ecological community in several locations in NSW and their slow rate of recovery from disturbance.