Toward the end of the 2001-2009 Millennium Drought, long-nosed fur seals (Arctocephalus forsteri) began entering the Lakes and Coorong waterways, a freshwater and estuarine system at the mouth of the Murray River in South Australia, where they rapidly made themselves unwelcome amongst commercial gillnet fishers. The seals frequented gillnets, removing catch and ripping holes in nets, and avoided all means of deterrent. Fifteen years on, we assessed the seal’s ecological and social impacts in the Lakes and Coorong region. The ecological assessment was based on seal abundances, foraging behaviour (GPS location recorders), diet (scat hard-part and DNA analyses) and ecosystem role (Ecopath modelling), while social impacts were inferred from reported interactions and changes in behaviour, of fishers and other users of the Lakes and Coorong. Results have application for the seal’s future within the Lakes and Coorong, and for ecosystem and marine resource management elsewhere.