Fisheries resources are linked to one another through complex food web and habitat interactions, such that harvest of one species could have impacts on others. However, fish stocks are assessed and managed on a case-by-case basis with little to no consideration for effects on other species. Ecosystem-based fisheries management (EBFM) calls for a more holistic approach that accounts for environmental drivers, food web interactions, and habitat associations. A major impediment to EBFM has been the perceived lack of data to support ecosystem models. Recently, concerted efforts have been made to enhance data collection, archival, discoverability, and access. As a result, ecosystem model development has become more efficient and transparent. Additionally, critical knowledge gaps have been identified. While many challenges remain, overcoming the data deficiencies is the first step towards advancing EBFM and enhancing management of complex fisheries ecosystems.