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Many fundamental processes in oceanic transport and limnology occur in geophysical flows that are both local in space and transient in time, and that require equally space and time-resolved methods of analysis. The importance of providing physics-based, quantitative modeling of such flows has driven the development of numerical methods for geophysical fluid dynamics for over three decades. Here, we use direct numerical simulations to investigate a range of stratified, particle-laden flows that are accurately described by the three-dimensional Navier-Stokes equations for an incompressible flow in the Boussinesq limit. We firstly investigate the propagation, transport and mixing dynamics of density-driven gravity currents moving in stratified environments. We propose new models for the intrusion of a turbidity current into a linearly stratified ambient based on three-dimensional simulations. We then describe the interaction between a gravity-current and an internal wave and characterize a phenomenological change in the long-term effect of the interaction at a critical wave height. We then quantify the role of double-diffusive processes in the Dead Sea in Summer and their role in the seasonality of salt crystallization and deposition. We also describe large-scale double-diffusive instabilities that arise in high-Prandtl sedimentary double-diffusive systems such as linearly stratified particle-laden salt water. Finally, we quantify mixing induced by a swarm of small-scale self-propelled organisms migrating in a stratified ambient fluid. We compare the relative contribution to mixing by individual swimmers within the swarm to that of the large-scale motion produced by the collective motion of the swarm.