Laboratory studies of ripples and dunes show robust relations between bedform geometry and both fluid flow conditions and grain size. These empirical relations are derived at equilibrium—defined by the achievement of stationary bedform statistics under a steady flow—and are used for both theoretical models and reconstructing paleoflow conditions from sedimentary deposits. In natural environments, however, the flow of water and wind is highly variable, and bedform patterns adjust in response by redistribution of mass. Disequilibrium may arise whenever the flow changes faster than bedforms can adjust. We review and synthesize recent findings on bedform disequilibrium for bedforms in three different cases: subaqueous unidirectional flows (primarily rivers), wave and combined wave–current flows, and aeolian flows. For all three cases, the bedform turnover time, which is the timescale to displace the entire sediment volume of a bedform, is the relevant timescale governing the adjustment of bed morphology to a changing flow. The mechanisms of adjustment, however, are not universal. Formation and annihilation of defects in the planform pattern occur in all systems, and these are the primary adjustment modes for oscillatory flows, which produce ripples that do not substantially migrate. However, collisional merging and calving are the primary mechanisms for the change of size and spacing of migrating bedforms in unidirectional flows (e.g., river and aeolian settings). Further, the mechanisms of bedform growth differ from the mechanisms of decay, causing hysteresis in the response of bedform size to a waxing then waning flow, which is a reflection of disequilibrium. Since the bedform turnover time is proportional to size, it is likely that the largest dunes in rivers and deserts are always out of equilibrium—and hence their size does not generally reflect the instantaneous flow conditions. We define a dimensionless bedform equilibrium number, T*, that characterizes the extent of adjustment and apply this idea to bedforms created in each flow type. Finally, we outline potential signatures of bedform disequilibrium in the sedimentary record, and how this information can be used to provide a richer interpretation of ancient deposits through paleoflow analysis. Ultimately, given the generally unsteady and nonuniform nature of natural flows, disequilibrium may be the norm in nature, and thus should be emphasized in the analysis of modern bedforms and interpretations of ancient strata.