The influence of algae presence in surface water on the settling velocities of microplastics is unknown, and determining it is challenging due to the turbidity of algal suspensions. Measuring the settling velocity of microplastics has traditionally relied on either manual measurement techniques or 2D Particle Tracking Velocimetry (PTV). This study introduces a 3D-PTV method tailored to determine the effects of algae (Synechoccocussp.) on microplastic settling speeds in semi-large columns. We demonstrated that 3D PTV produces much more accurate results than 2D particle tracking. Testing the method in six experiments with varying algae concentrations revealed consistent results across the experiments and alignment with some theoretical approximations. The results were concurrent with calculated 2D speeds. No influence of algal density on settling velocities was found, which is highly relevant for microplastic fate modeling in eutrophic systems. We highlight the applicability and accuracy of 3D particle tracking velocimetry in further understanding microplastic settling behavior.