The formation of bacterial biofilms on solid surfaces within a fluid starts when bacteria attach to the substrate. Understanding environmental factors affecting the attachment and the early stages of the biofilm development as well as the development of active methods of biofilm control are crucial for many applications. Here we show that biofilm formation is strongly affected by the hydrodynamics of flows generated by surface waves in layers of bacterial suspensions. Deterministic wave patterns promote the growth of patterned biofilms while wave-driven turbulent motion destroys the patterns. The location of the attached bacteria on a solid substrate differs from the settlement location of inactive bacteria and of the passive micro-particles: strong biofilms form under the wave antinodes while passive particles and inactive bacteria settle under nodal points. By controlling the wave lengths and horizontal mobility of the wave patterns, one can either shape the biofilm formation and enhance the biofilm growth, or discourage the formation of biofilm patterns. The results suggest that the deterministic wave-driven transport, rather than hydrodynamic forces, determine the preferred location for the bacterial attachment.