The wave-driven floating photobioreactors (PBRs) with advantages of easy in scaling-up, low energy inputs and low fabricating cost, hold great potential for massive and cost-energy effective microalgae production. However, their applications may be seriously challenged by intermittent waves that could produce very poor mixing under poor wave conditions, leading to a significant reduction of biomass productivity or even collapse of the cultures. To improve the utilization efficiency of waves for efficient and stable microalgae production in the floating PBRs, this work aims at numerically studying the fluid-dynamics of the floating PBRs, as well as the effects from wave conditions, culture depth and three different PBRs’ structures of square, rectangular and circular types. The results showed that the liquid inside the floating PBRs follow a periodic sinusoidal and reciprocating flow, and the square PBR had aggressive mixing characteristics at high wave excitation frequency, while the rectangular PBR produced more intense mixing at low wave excitation frequency. Regarding the culture depth, the dependence of liquid mixing on the culture depth showed a decreasing trend. Moreover, the results indicated that the PBRs with a high culture depth had several dead zones, although there was apparent upward flow at the high excitation frequency. This work provides valuable insight into increasing the utilization efficiency of wave energy for mixing enhancement in the floating PBRs and their design.