The Maximum Entropy Theory of Ecology (METE) predicts the shapes of macroecological metrics in relatively static ecosystems, across spatial scales, taxonomic categories and habitats, using constraints imposed by static state variables. In disturbed ecosystems, however, with time-varying state variables, its predictions often fail. We extend macroecological theory from static to dynamic by combining the MaxEnt inference procedure with explicit mechanisms governing disturbance. In the static limit, the resulting theory, DynaMETE, reduces to METE but also predicts a new scaling relationship among static state variables. Under disturbances, expressed as shifts in demographic, ontogenic growth or migration rates, DynaMETE predicts the time trajectories of the state variables as well as the time-varying shapes of macroecological metrics such as the species abundance distribution and the distribution of metabolic rates over individuals. An iterative procedure for solving the dynamic theory is presented. Characteristic signatures of the deviation from static predictions of macroecological patterns are shown to result from different kinds of disturbance. By combining MaxEnt inference with explicit dynamical mechanisms of disturbance, DynaMETE is a candidate theory of macroecology for ecosystems responding to anthropogenic or natural disturbances.