Orbital shakers are used extensively to mix and aerate fluids in the laboratory. A recently new application of orbital shakers is to use the time-dependent wall-shear stresses that occur in the shaker as a proxy for blood flow. This significantly simplifies the study of quantifying the response of cell cultures to mechanical stresses, which is thought to be an important factor for cardiovascular diseases such as atherosclerosis. The flow inside the orbital shaker is however far from being fully understood, particularly in the non-linear regimes in which the experiments take place. The research focuses on analysing using numerical simulations the variety of patterns -from single and multiple crested waves to breaking waves- originated under different operating parameter. Also, an analytical approach taken from sloshing dynamics has been used to understand the weakly shaken cases. The aim of the project is twofold: to provide a guideline to design simulations under the current configuration for different operating parameters, and to propose an optimised configuration of the orbital shaken cell cultures.