Marine macrophytes are vertically distributed according to their ability to optimize their photosynthetic performance. We assessed the photo-physiological performance of the seagrass Cymodocea nodosa and the green seaweed Caulerpa prolifera at varying depth at Gran Canaria Island (Canary Islands, eastern Atlantic). The biomass of C. nodosa decreases with depth, while the opposite occurs for C. prolifera. Photochemical responses of both macrophytes were measured in shallow (5 m) and deep (20 m) waters at two times via chlorophyll a fluorescence and internal content of photoprotective pigments and antioxidant activity. We additionally carried out a reciprocal transplant experiment by relocating shallow and deep vegetative fragments of both macrophytes to assess their short-term photo-physiological acclimation. Overall, C. nodosa behaves as a ‘light-plant’, including a larger optimum quantum yield and ETRmax under scenarios of high photosynthetically active radiation and a larger antioxidant activity. In contrast, C. prolifera is a ‘shade-adapted’ plant, showing a larger carotene content, particularly in shallow water. Deep-water C. nodosa and C. prolifera are more photochemically efficient than in shallow water. The alga C. prolifera shows a rapid, short-term acclimation to altered light regimes in terms of photosynthetic efficiency. In conclusion, decreased light regimes favour the photosynthetic performance of the green alga when both species coexist.