Fish Aggregating Devices (FADs) are man-made floating objects deployed by fishers to attract tuna and improve their catches. Currently, more than half of the global tropical tuna purse-seine catches occur at FADs. The fast development of the purse-seine fisheries operating on drifting FADs (DFADs) has raised concerns regarding their impacts on tuna populations, on non-target species like sharks, as well as on pelagic and coastal habitats. Consequently, the management of DFAD fisheries is a priority of all tuna regional fisheries management organizations. Limits on the number of DFADs have been set in all oceans, based on the precautionary approach, due to the little availability of science-based advice to support management decisions. This paper discusses a science-based framework for the management of DFADs, relying on indicators and operating models. A set of indicators and models related to the ecological impacts of DFADs is discussed, considering the case study of DFAD fisheries management in the Indian Ocean. The aim of this approach is assessing and predicting the effects of increasing numbers of DFADs on coastal and pelagic ecosystems, in order to support and/or evaluate past, present and future management actions.