This paper presents a multi-physics modeling methodology for the quantitative prediction of microalgae productivity in raceway ponds by combining a semi-mechanistic model of microalgae growth describing photoregulation, photoinhibition and photoacclimation, with models of imperfect mixing based on Lagrangian particle-tracking and heterogeneous light distribution. The photosynthetic processes of photoproduction, photoregulation and photoinhibition are represented by a model of chlorophyll fluorescence developed by Nikolaou et al. (2015), which is extended to encompass photoacclimation. The flow is simulated with the commercial CFD package ANSYS, whereas light attenuation is described by the Beer-Lambert law as a first approximation. Full-scale simulation results are presented on extended time horizons. Comparisons are made in terms of areal productivities under both imperfect and idealized (CSTR) mixing conditions, and for various extraction rates and water depths.