Lakes, ponds, reservoirs, and flowing waters are dynamic systems in which organisms live and grow and diverse biogeochemical reactions occur. Through theory, experimentation, in the laboratory and in the field, and modeling, the mechanisms influencing the flow of water have been identified and evaluated. Here we describe pertinent physical processes, in particular turbulence, and its influence on dispersion and mixing. Wind, heating and cooling, and the flow of water generate larger-scale flows, such as currents, organized spiral motions, surface waves, density-driven flows, and internal waves. We describe these processes and provide equations pertinent to quantifying them and the time scales over which they occur. We provide examples of the temporal and spatial variability of the flows and their importance for ecosystem processes. We illustrate how one- and three-dimensional hydrodynamic models can be used for predictions of changes in the hydrodynamics of lakes over time and in ecosystem studies.