When cultivated properly in bioreactors, microalgae have been found to produce vast amounts of biomass. In the case of diatom cultivation where the organisms will fall out of suspension quite easily, paddle wheels or pumps are the primary means to maintain the necessary velocity in the raceway. This study will focus on the potentially harmful shear stress these devices may impart onto the organisms. The system used to impart shear stress to a diatom culture was a cone and plate viscometer. Cells were counted using a fluorescein diacetate staining method with a fluorescent and brightfield microscope. Under the white light all cells were visible while only the healthy cells were visible under fluorescent light. The sample was exposed to shear stress with the cone and plate viscometer at 6 Pascals for 10 minutes and compared against a non-sheared sample. For each sample, 5 pairs of white and fluorescent light images were captured, counted, and averaged. A non-sheared sample was paired with a sheared sample to calculate the decrease in cell viability. The slope was calculated from the plot of shear stress and cell viability for 9 strains. In each case shear stress resulted in a significant decrease in cell viability; however, there was no statistical difference between strains. While effective, this method would be impractical for a commercial algae cultivation facility as the viscometer in this study costs approximately $100,000. Therefore, tests were performed to determine if a rotary mixer could be substituted for the viscometer. The hypothesis was that the cell damage was a product of shear stress and exposure time. For the viscometer test, the shear exposure was 3600 Pa s. Two rotational mixer tests were performed, one at 1250 RPM for 7 hours and one at 313 RPM for 28 hours, providing the same 3600 Pa s shear exposure. After staining, cell viability decreased 35.62% and 11.07% in the 1250 RPM and 313 RPM test, respectively. This difference was significant compared to the 6.04% decrease in the viscometer test. The increased cell damage was attributed to turbulence in the mixer tests and the basis for further study.