Abstract Previous ecological models for disturbance from energetic perspectives have focused on destructive pulses by which storages in a system are quickly drained during disturbance events and recovered thereafter. However, considering the wide range of disturbance intensities, frequencies, and durations in nature, disturbance effects on ecosystem energetics would be better understood by diversifying the disturbance effects on specific system configurations or energy pathways. Based on two hypotheses, we built simulation models of the variable disturbance–productivity relationships observed in a freshwater aquatic microcosm study. First, we hypothesized that disturbances will differentially alter the intrinsic rates of energy pathways in a system. Second, we hypothesized that there is a disturbance threshold where response of the intrinsic rates changes abruptly. Simulation results showed variable patterns of gross primary productivity (GPP) during the disturbance and post-disturbance periods under the diverse scenarios of disturbance effects on the intrinsic rates. Simulation results confirmed that the second hypothesis (i.e., disturbance threshold) was essential to achieve a U-shaped or peaked disturbance–productivity relationship. We evaluated the models by comparing them with the results of the microcosm tests, and suggested possible mechanisms of the variable disturbance–productivity relationships by varying parameters related to the disturbance effects on the intrinsic rates and the disturbance thresholds.