The current research presents a mathematical model to study the flow of a non-Newtonian magnetohydrodynamics (MHD) Casson-Carreau nanofluid (CCNF) over a stretching porous surface, considering mass and heat transport rates with Stefan blowing, non-linear thermal radiation, heat source-sink, chemical reaction, thermophoretic and Brownian motions, convective heating, Joule heating, motile microorganisms, and bio-convection. The presence of microorganisms is utilized to control the suspension of nanomaterials within the nanofluid. The current flow model has been rendered by the boundary layer approximation and we get the highly nonlinear partial differential equations (PDEs). These nonlinear PDEs are simplified by the novel Lie group theoretic method. The one-parameter Lie scaling method simplified the PDEs and convert it into the ordinary differential equations (ODEs). Numerical solutions for these ODEs are obtained using the bvp4c scheme built-in function in MATLAB, ensuring reliable outcomes for temperature, velocity, concentration, and motile microorganism density profiles. The numerical results are presented through graphs and compared with available data, showing good agreement. These numerical outcomes reveal several important flow characteristics. Rates of change for Nr are 0.0007 and 0.0005, and for Ω, they are −0.0754 and −0.0536, respectively. Similarly, the rate of change for Rb in both models is −0.002 and −0.0002. Analysis shows a positive impact of the bioconvection Rayleigh number in both models, notably higher for the Casson fluid compared to the Carreau fluid model. Buoyancy ratio parameter exhibits consistent rates of change, while the reduction in impact is more pronounced for the Casson fluid model in the case of the mixed bioconvection parameter. The mixed bio-convection parameter reduces momentum velocity for both Casson and Carreau fluids, whereas the Darcy parameter boosts fluid velocity. As the Newtonian heating parameter increases, the temperature velocity distribution of both fluids also increases. The concentration profile of both Casson-Carreau fluid phases declines as the heat source-sink parameter and Schmidt number increase. Microbial velocity shows a decrease with increasing R values, whereas the opposite trend is observed for the Peclet number Pe.