Biofuel production from microalgae represents an acute optimization problem for industry. There is a wide range of parameters that must be taken into account in the development of this technology. Here, mathematical modelling has a vital role to play. The potential of microalgae as a source of biofuel and as a technological solution for CO2 fixation is the subject of intense academic and industrial research. Large-scale production of microalgae has potential for biofuel applications owing to the high productivity that can be attained in high-rate raceway ponds. We show, through 3D numerical simulations, that our approach is capable of discriminating between situations where the paddle wheel is rapidly moving water or slowly agitating the process. Moreover, the simulated velocity fields can provide lagrangian trajectories of the algae. The resulting light pattern to which each cell is submitted when travelling from light (surface) to dark (bottom) can then be derived. It will then be reproduced in lab experiments to study photosynthesis under realistic light patterns.