A simulation manager in HEC-FIA is a combination of individual simulations. A simulation connects an alternative with an event and a time window. The user can add the same alternative for multiple events, allowing the events to be run in the same simulation group. Alternatively, multiple alternatives can be matched to the same event, allowing the evaluation of damages to be based on changes in the floodplain (such as structural and nonstructural measures) identified in the alternative, through the watershed configuration or other changes in the alternative.

When computing damages for a single event in HEC-FIA, all structures are assumed to be fully valued. However, under some conditions, it could be the case that structures had been recently flooded by a separate event. HEC-FIA Version 3.1 added the new reconstruction compute option to facilitate in the analysis of computing an estimate of damages for the second event (or multiple subsequent events) where structures are in the process of being reconstructed from the first (or previous) event.