Post-disturbance patterns in freshwater community reassembly can be affected by a multitude of factors including regional species pools, time since disturbance, local habitat, anthropogenic stressors, and species’ life histories. However, community reassembly patterns and the time scales over which they occur remain poorly understood for freshwater mussels. Here we utilize mussel occurrence and abundance data from 20 disturbed and 47 undisturbed (i.e., reference) sites to characterize temporal dynamics in community composition and species abundances relative to site disturbance. Changes in community composition, as well as rates in composition change, were site-specific and varied substantially across sites relative to disturbance status and time between sampling events. Community trajectory analyses revealed idiosyncratic site trajectories with respect to both community composition and abundance. Disturbed site trajectories indicated these sites were unlikely to return to either pre-disturbance community composition or abundances in the timeframes considered here. Ecological state assessment developed reference envelopes that can be leveraged to determine if sampling events or entire trajectories in disturbed sites differ exceptionally in mussel community compositions and abundances. Multiple sampling events in disturbed sites were found to fall outside this reference envelope. Ultimately, results of this investigation will aid managers in defining expectations for community reassembly and recovery, identifying conservation actions necessary to reach conservation goals, and developing tools for identifying whether disturbed sites are beginning to return to baseline or reference expectations with respect to mussel community composition or abundances. To this end, new perspectives about what constitutes mussel community recovery, and how recovery is assessed, will likely need to be adopted.