As part of ongoing commitments to produce electricity from renewable energy sources in Scotland, Orkney waters have been targeted for potential large-scale deployment of wave and tidal energy converting devices. Orkney has a well-developed infrastructure supporting the marine energy industry; recently enhanced by the construction of additional piers. A major concern to marine industries is biofouling on submerged structures, including energy converters and measurement instrumentation. In this study, the marine energy infrastructure and instrumentation were surveyed to characterise the biofouling. Fouling communities varied between deployment habitats; key species were identified allowing recommendations for scheduling device maintenance and preventing spread of invasive organisms. A method to measure the impact of biofouling on hydrodynamic response is described and applied to data from a wave-monitoring buoy deployed at a test site in Orkney. The results are discussed in relation to the accuracy of the measurement resources for power generation. Further applications are suggested for future testing in other scenarios, including tidal energy.