Controlled manipulation of micro- and nanoparticles is important in numerous biological and chemical studies. In this dissertation, I present my work on manipulating micro- and nanoparticles using acoustics for two different applications – a) Separating nanoparticles based on their size, and b) Tuning shear thickening in colloidal suspensions. In Chapter 2, I present a novel surface acoustic wave (SAW)-based microfluidic device that enables size-based separation of nanoparticles using acoustic forces. Acoustofluidics is a promising technique to separate biological nanoparticles (e.g. extracellular vesicles); however, such separations have been challenging because of the competing nature of the acoustic radiation force and acoustic streaming on the nanoparticles. I present a device that overcomes these challenges and demonstrates a continuous-flow separation of particles on the order of 100 nm. I also discuss an analytical stochastic method that accounts for particle diffusion to accurately model the transport of nanoparticles in such devices. I intend this device to be used for broad range of biological and chemical applications that require sorting of nanoparticles, and the analytical method to accurately predict the nanoparticle transport in such systems. In Chapter 3, I present the first practical method, which uses acoustic perturbations, to actively tune the shear thickening behavior on demand. Shear thickening is a non-Newtonian phenomenon where the viscosity of a colloidal suspension increases upon application of shear stress or strain rate. The shear-thickening viscosity is difficult to control actively in the industrial processes. In this chapter, I use piezoelectric transducers to apply acoustic perturbations to a shear thickening suspension to tunably reduce its viscosity. I attribute the mechanism of dethickening to the disruption of shear-induced network of particles, called force-chains, by the perturbations. This method can be easily integrated with the existing flow geometries, which makes it a powerful tool for actively controlling the flow properties of shear thickening suspensions. In Chapter 4, I extend the method developed in Chapter 3 to elucidate the dynamics of the dethickened states. Understanding the fundamental physics of these states is crucial for designing the optimal dethickening protocols. In this chapter, I show that the fully dethickened states behave strikingly different from that of the partially dethickened states. I find that the viscosity level of a fully dethickened state can be maintained by turning the perturbations off intermittently, whereas that is not possible in a partially dethickened state. I provide microscopic insights into this behavior using the hyperuniformity framework. Because of the dynamical differences between the two states, I show that the parameters governing optimal dethickening are different for each state. This work paves the way for designing smart dethickening protocols for practical applications.