Increasing concerns over global climate change and sustainable fuel procurement are driving the search for new ways to derive energy from the seas. Globally, the offshore wind energy sector has progressed rapidly, and wave and tidal-current energy converters are now approaching deployment at commercial scales. To date, most studies of the ecological effects of marine renewable energy development have concentrated on birds and marine mammals. Here, we focus on the consequences for benthic flora and fauna, and for benthic habitats across a variety of scales. We use a Benthic Footprint concept to discuss the potential for species-specific environmental responses, and to consider the poorly understood cumulative effects of wind, wave, and tidal-current energy operations on marine ecosystems. Collaborations between ecologists, industry specialists, and government bodies, as well as better designs for devices, arrays, and developments consisting of multiple arrays, can contribute to the goal of reducing the Benthic Footprint of marine renewable energy, thereby facilitating large-scale implementation of these technologies.