Microalgae cultivation is considered as one of the promising technologies for CO2 utilization and the biomass can be further used for the production of biofuels or high-value products. The processes of harvesting and dewatering of produced microalgae are complex since the microalgae cells are very small and the density is similar to the density of the culture medium. The separation has a major impact on the total biomass production cost. It is not possible to determine one separation system that is the most appropriate for specific microalgae species. In this paper, a methodology for the design of harvesting and dewatering equipment was developed based on the measured settling velocity and microalgae cell size. Sedimentation tests and distribution of particles were performed for different algal concentrations. This work describes the design methodology of the separation units for the primary harvesting and dewatering of microalgae mixture by gravitational and centrifugal forces. The basic design parameters of separation systems were selected according to the three demonstrative applications. The rest of the basic parameters were defined based on the developed design methodology and geometrically similar existing industrial equipment. Limitations of individual systems for the given configurations were emphasized. The disc centrifuge seems to be the most appropriate equipment for the selected demonstrative systems.