If you are seeking methods for mapping the extent and coverage of reef forming species mussels and oysters many of the acoustic techniques will work well. Even some of the relatively simple single beam ground discrimination techniques should work well. Although on their own will not tell you much about the condition and overall health of the beds without good ground truthing.
Their are some good guides on video surveying etc such as the MESH Handbook
Caddell, S. E, Service MatthewDetermining the activity patterns and potential seabed impact of aquaculture: The example of blue mussel culture in Belfast Lough, Northern Ireland.
Adele Boyd, Annika Clements, Heather Moore, Rhys Cooper,Meredith Scanlon, Matthew Service
ICES Annual Science Conference 2014; 09/2014
Using Optimum Allocation Analysis to Improve Seed Mussel Stock Assessments
James Asa Strong, Matthew Service
Journal of Shellfish Research 04/2011; 30(Apr 2011):1-6.
An Acoustic Bottom Classification Survey of Strangford Lough, Northern Ireland
B.H. Magorrian, M. Service, W. Clarke
Journal of the Marine Biological Association of the UK 10/1995; 75(04):987 - 992.
Acoustic mapping of Shellfish Habitats
5th Int Conference on Remote Sensing for Marine and Coastal Environments, San Diego; 01/1998