In this work, we focus on the motility behavior of two model micro-organisms widely used in the study of active fluids: Chlamydomonas reinhardtii micro-alga and Synechocystis sp. cyanobacterium. Understanding the physiological responses of micro-organisms under variable environmental conditions is essential for bioreactor engineering. Yet, most of the previous studies focused on the observation of cellular motility regardless of the growth process. Here, we measure the motility of Chlamydomonas reinhardtii and Synechocystis sp. during their growth when subjected to different intensities of hydrodynamic shear stress. The results demonstrate a significant difference in the motility response of the two species against the applied hydrodynamic shear stress. Mechanical agitation appears to affect the motility of Chlamydomonas reinhardtii micro-algae by stimulating the growth process and increasing the magnitude of the cellular swimming velocity. This effect is described using an empirical model for the time variation of the motility. Synechocystis cells show a high endurance to the applied shear such that the global effect of agitation intensity on their motility is insignificant. However, it seems that the peak of the swimming velocity always occurs in the middle of exponential phase of growth.