Using a thermally stratified water-based nanofluid and a permeable stretching sheet as a simulation environment, this research examines the impact of nanoparticle aggregation on MHD mixed convective stagnation point flow. Nanoparticle aggregation is studied using two modified models: the Krieger-Dougherty and the Maxwell-Bruggeman. The present problem's governing equations were transformed into a solvable mathematical model utilizing legitimate similarity transformations, and numerical solutions were then achieved using shooting with Runge-Kutta Fehlberg (RKF) technique in Mathematica. Equilibrium point flow toward permeable stretching surface is important for the extrusion process because it produces required heat and mass transfer patterns and identifies and clarifies fragmented flow phenomena using diagrams. Nanoparticle volume fraction was shown to have an impact on the solutions' existence range, as well. Alumina and copper nanofluids have better heat transfer properties than regular fluids. The skin friction coefficients and Nusselt number, velocity, temperature profiles for many values of the different parameters were obtained. In addition, the solutions were shown in graphs and tables, and they were explained in detail. A comparison of the current study's results with previous results for a specific instance is undertaken to verify the findings, and excellent agreement between them is observed.