In this article, unsteady free convective heat transport of copper-water nanofluid within a square-shaped enclosure with the dominance of non-uniform horizontal periodic magnetic effect is investigated numerically. Various nanofluids are also used to investigate temperature performance. The Brownian movement of nano-sized particles is included in the present model. A sinusoidal function of the y coordinate is considered for the magnetic effect, which works as a non-uniform magnetic field. The left sidewall is warmed at a higher heat, whereas the right sidewall is cooled at a lower heat. The upper and bottom walls are insulated. For solving the governing non-linear partial differential equation, Galerkin weighted residual finite element method is devoted. Comparisons are made with previously published articles, and we found there to be excellent compliance. The influence of various physical parameters, namely, the volume fraction of nanoparticles, period of the non-uniform magnetic field, Rayleigh number, the shape and diameter of nanoparticles, and Hartmann number on the temperature transport and fluid flow are researched. The local and average Nusselt number is also calculated to investigate the impact of different parameters on the flow field. The results show the best performance of heat transport for the Fe3O4-water nanofluid than for other types of nanofluids. The heat transport rate increases 20.14% for Fe3O4-water nanofluid and 8.94% for TiO2-water nanofluid with 1% nanoparticles volume. The heat transportation rate enhances with additional nanoparticles into the base fluid whereas it decreases with the increase of Hartmann number and diameter of particles. A comparison study of uniform and non-uniform magnetic effects is performed, and a higher heat transfer rate is observed for a non-uniform magnetic effect compared to a uniform magnetic effect. Moreover, periods of magnetic effect and a nanoparticle’s Brownian movement significantly impacts the temperature transport and fluid flow. The solution reaches unsteady state to steady state within a very short time.