Thermodynamic function Exergy, which represents the distance of an open system from equilibrium, is proposed as an ecological indicator for summarizing the complex dynamics occurring in a disturbed community during the recovery processes. This quantity has been difficult to capture using classical indices. Exergy storage is estimated for benthic communities in response to experimental disturbance, as induced by ecological engineering, at the Chongxi tidal wetland of Chongming Island. Exergy storage was sampled using the BACI scheme (before versus after, control versus impact). The control area is proposed as a dynamic reference for estimating the local Exergy storage of the benthic community. Three different methods were used for estimating Exergy on the basis of coefficients: (a) taken from trophic groups, (b) estimated from coding genes for broad taxonomical groups and (c) estimated from genome size and taken as close as possible to the taxonomical level of the species, providing a basis for inferring upon their similarities. The results show a decrease of local exergy content in the disturbed area, with a minimum in the area exposed to the engineering 1 month after the experimental disturbance. Subsequently, the Exergy of the benthic community increased to the reference level, i.e., the surrounding control area, in accordance with the proposed hypothesis on the dynamics of Exergy storage during a system′s development. Moreover, the adjacent control samples represented an appropriate dynamic reference for estimating the local Exergy of the experimentally disturbed community. The three methods for estimating the local Exergy values provided comparable results. Therefore, we discuss the feasibility of using the more available genome size data set for estimating Exergy and the broader implications of using this indicator in other biological systems. Exergy was demonstrated to be a useful indicator that integrates the processes underlying the recovery of the benthic community after disturbance.