The drive towards sustainable energy has seen rapid development of marine renewable energy devices (MREDs). The NERC/Defra collaboration FLOw, Water column and Benthic ECology 4-D (FLOWBEC-4D) is investigating the environmental and ecological effects of installing and operating wave and tidal energy devices. The FLOWBEC sonar platform combines several instruments to record information at a range of physical and multitrophic levels for durations of two weeks to capture an entire spring-neap tidal cycle. An upward-facing multifrequency Simrad EK60 echosounder is synchronized with an upward-facing Imagenex Delta T multibeam sonar. An acoustic Doppler velocimeter (ADV) provides local current measurements and a fluorometer measures chlorophyll (as a proxy for phytoplankton) and turbidity. The platform is self-contained, facilitating rapid deployment and recovery in high-energy sites and flexibility in gathering baseline data. Five 2-week deployments were completed in 2012 and 2013 at wave and tidal energy sites, both in the presence and absence of renewable energy structures at the European Marine Energy Centre (EMEC), Orkney, U.K. Algorithms for target tracking have been designed and compared with concurrent, shore-based seabird observations used to ground truth the acoustic data. The depth preference and interactions of birds, fish schools and marine mammals with MREDs can be tracked to assess whether individual animals face collision risks with tidal stream turbines, and how animals generally interact with MREDs. These results can be used to guide marine spatial planning,device design, licensing and operation, as different device types are tested, as individual devices are scaled up to arrays, and as new sites are considered.