Abstract Collisions between traffic and wildlife can have population-level consequences and carry economic costs. Vessel-strike may threaten the viability of whale populations especially where habitat overlaps with frequent vessel traffic; as seen in the Hauraki Gulf, New Zealand, which is the entrance to the busy Ports of Auckland and holds a year-round population of endangered Bryde’s whales (Balaenoptera edeni). Here, we identify a serious threat: out of 44 Bryde’s whale-deaths, 17 of 20 (85%), with known cause of mortality, sustained injuries consistent with vessel-strike; a mortality rate that is likely to be unsustainable. This information started a social forum with stakeholders engaged in science-based discussion of mitigation measures to reduce lethal vessel-strikes in this region. To determine the viability of different mitigation actions we studied Bryde’s whale behavior with suction-cup attached tags. Tagged whales (n = 7, 62.5 h) spent 91% of their time at depths within the maximum draft of vessels transiting the Gulf, increasing the probability of vessel-strike. Whales are broadly distributed throughout the Gulf so re-routing traffic would not lessen the threat of vessel-strike. Monitoring whales visually is difficult and not applicable at night, when whales rested closer to the surface than during the day. Passive acoustic monitoring is unreliable due to the whales’ low vocal activity and because low frequency calls are susceptible to masking from vessel noise. These findings resulted in a Transit Protocol for Shipping including voluntary speed restrictions and a monitoring plan, highlighting the value of scientific and social stakeholders working together for conservation.