Effective management of natural resources involves a multidisciplinary perspective to address complex issues in data poor-environments. With mobile species that do not conform to human-defined borders a cross-boundary approach is essential. There is a continuing concern of ecological sustainability of marine environments, which demands monitoring of ecosystem indicators. Such indicators are increasingly derived from monitoring sentinel species. Harbour porpoises (Phocoena phocoena) are included as indicator species in several national and international agreements. Increasing exposure to anthropogenic stressors may impact harbour porpoise populations. To investigate these risks, a better understanding of threats and their effect is required. This study aimed to identify current knowledge gaps, to predict future pressures or threats, and to define useful conservation indicators to facilitate future research on harbour porpoises in the North Sea, through expert elicitation gained in a two-round Delphi approach. The three most important knowledge gaps addressed were bycatch, population dynamics, and the cumulative effects of multiple stressors. Bycatch was predicted as the highest concern for porpoises in the next 20 years, followed by chemical and noise pollution, respectively. A list of essential indicators aiming to increase understanding of harbour porpoises’ health status was established and studying causes of death, distribution, abundance, habitat use and diet composition were scored as most relevant. These results should guide research focus and management objectives of harbour porpoise populations and the study design could be translated to serve managers in other geographical areas aiming to identify knowledge gaps and defining research priorities for other wildlife species.