Seagrasses are flowering plants, adapted to marine environments, that are highly diverse in the Mediterranean Sea and provide a variety of ecosystem services. It is commonly recognized that light availability sets the lower limit of seagrass bathymetric distribution, while the upper limit depends on the level of bottom disturbance by currents and waves. In this work, detailed distribution of seagrass, obtained through geoacoustic habitat mapping and optical ground truthing, is correlated to wave energy and light on the seafloor of the Marine Protected Area of Laganas Bay, Zakynthos Island, Greece, where the seagrasses Posidonia oceanica and Cymodocea nodosa form extensive meadows. Mean wave energy on the seafloor was estimated through wave propagation modeling, while the photosynthetically active radiation through open-access satellite-derived light parameters, reduced to the seafloor using the detailed acquired bathymetry. A significant correlation of seagrass distribution with wave energy and light was made clear, allowing for performing fine-scale predictive seagrass mapping using a random forest classifier. The predicted distributions exhibited >80% overall accuracy for P. oceanica and >90% for C. nodosa, indicating that fine-scale seagrass predictive mapping in the Mediterranean can be performed robustly through bottom wave energy and light, especially when detailed bathymetric data exist to allow for accurate estimations.