Most coral reef remote sensing has used optical sensors which are of very limited value in high turbidity environments. These limitations are now being overcome through the deployment of acoustic remote sensing methods. Active sonar sensors are usually towed behind a boat and measure the depth of the water and components of surface roughness and hardness (White et al., 2003). Compared to optical methods, these sensors have the following advantages; (i) greater depth of penetration, (ii) unconstrained by optical water properties, and (iii) measurement of sea bed structure, which may be particularly important for specific organisms such as reef fish. However, disadvantages of the methods include; (i) they cannot be deployed in shallow water (