Antarctic krill is a keystone species in the Antarctic marine ecosystem and the target of a growing fishery. Given the ecological importance of krill, concerns have been raised about potential negative impacts of fishing on the Southern Ocean ecosystem. Resource-efficient approaches to fisheries monitoring are particularly valuable in this context due to the high costs associated with data collection in Antarctica. In this study, we trained a segmentation model (U-Net) to extract dives of air-breathing krill predators from more than 30,000 h of active acoustic data collected by three krill fishing vessels over six years. We were able to characterize the temporal and spatial dynamics of predator-vessel co-occurrences, which aligned well with the findings from more costly tracking studies. For example, we found that encounters with whales consistently peaked in autumn around the Antarctic Peninsula, when whales are building up fat reserves for their migration to breeding grounds. We also demonstrated that protection measures, introduced to protect breeding penguins at the Antarctic Peninsula, have simply shifted penguin-vessel encounters to the South Orkney Islands, where the affected colonies are not currently monitored. Our approach, results, and application example demonstrate how acoustic data from fishing vessels can provide important information to support fisheries management. As a by-product of fishing operations, these data are cost-effective, offering unique temporal and spatial coverage and providing a useful basis for rapid, low-level assessments of the fishery's interaction with the wider ecosystem. This is particularly important given the unpredictable dynamics of krill fishery management decision-making.