The 3D bioprinting of aquatic photosynthetic organisms holds potential for applications in biosensing, wastewater treatment, and biofuel production. While algae cells can be immobilized in bioprinted cell‐friendly matrices, there is a knowledge gap regarding the thresholds of hydrodynamic shear stress that affect the cells’ functionality and viability during bioprinting. This study examines the effect of hydrodynamic shear stress on the fate of Chlamydomonas reinhardtii cells. Computational fluid dynamics models based on the Navier–Stokes equations are developed to numerically predict the shear stresses experienced by the cells during extrusion. Parallelly, cell culture experiments are conducted to evaluate the functionality, growth rates, and viability of algae cells within bioprinted constructs. By correlating cell culture and simulation results, the causal link between shear stress in the nozzle and cell viability and function has been characterized. The findings highlight that cell viability and function are significantly impacted by process factors. Notably, algae cell function is more sensitive to shear stress than cell viability. Functional impairments occur at maximum shear stresses around 5 kPa, while viability remains unaffected. Beyond 14 kPa, both functionality and viability decline significantly and irreversibly. The results emphasize the importance of assessing viability and function after bioprinting, rather than just viability.