Microalgal cultivations present challenges for monitoring and process control posed by their large scale and the likelihood that they will be composed of multiple species. Cell concentration is a fundamental parameter in any cultivation but is typically measured using off-line methods that may be time-consuming, laborious, or subject to interferences. Here, an in-situ microscope has been adapted for monitoring microalgal cultivations by adding a flow-through cell and adjusting image-processing algorithms. After installation in the bypass of a photobioreactor, the microscope enabled the continuous, automated acquisition of cell count, cell size, and cell morphology data on-line during cultivation processes over a period of 20. days, without sampling. The flow-through microscope was tested in cultivations of Chlamydomonas reinhardtii and Chlorella vulgaris. Cell concentration measurements were in agreement with off-line optical density measurements for both species. In addition, cell size and morphology distributions were obtained that revealed population shifts during the cultivation of C. vulgaris. This monitoring system thus provides a means to obtain detailed, non-invasive insights of microalgal cultivation processes.