Acoustofluidics has recently been popularized as a crucial element of lab-on-a-chip (LoC) platforms to efficiently manipulate microparticles and continuous matter alike. In this study, a three-dimensional (3D) numerical model is proposed to simulate the focusing of polystyrene microparticles with three diameters and micromixing of dilute species using two orthogonally oriented standing waves, contrasting them with one-dimensional (1D) waves. The limiting velocity method is modified to explore the 3D acoustic streaming in a symmetric microchannel. In contrast to 1D standing acoustic waves, the simultaneous excitation of two orthogonal waves generates an acoustic streaming velocity field that does not counteract the radiation force. The obtained results show that the focusing efficiency of 5-μm particles reaches 97% with two dimensional (2D) standing acoustic waves, which was unachievable using 1D waves. Moreover, by reducing the flow rate to 1 μL min−1, the focusing of critical microparticle diameter peaked at 94%, indicating an approximately 9% improvement over a flow rate of 2.5 μL min−1. Increasing the viscosity of the background fluid resulted in 16% better 2D focusing with a single vortex compared to other cases, and higher amplitudes did not change focusing efficiency with a single vortex, while reducing efficiency in other cases. Finally, using 2D acoustic waves remarkably improved the mixing efficiency of dilute species, underscoring the advantage of 2D acoustic waves over their 1D counterpart. The proposed numerical model can play a meaningful role in cutting fabrication costs of next-generation LoC devices by identifying the most crucial parameters influencing acoustofluidic matter transport.