Vessels cause considerable disturbance to cetaceans world-wide, with potential long-term impacts to population viability. Here we present a comprehensive review of vessel impacts to cetacean behavior in Australian waters (2003–2015), finding inadequate protections to be in place. The majority of these studies found trends of decreased animal travel and resting behavioral states as well as low compliance to regulations, and they recommended further regulatory action such as greater enforcement or monitoring, or passive management strategies. As a case study, we conducted the first field assessment of vessel compliance with the Wildlife (Marine Mammal) Regulations 2009 in Gippsland Lakes, Australia, and provide the first assessment of the endangered Gippsland Lakes Burrunan dolphin (Tursiops australis) population’s behavioral ecology. Dolphin behavior and vessel regulation compliance data were collected during boat-based surveys of Gippsland Lakes from July 2017 to January 2018, with a total of 22 dolphin group sightings resulting in 477 five-minute point samples. 77% of dolphin sightings involved vessel interactions (within 400 m), and 56 regulation breaches were observed. These breaches were most severe in summer (mean = 4.54 breaches/hour). Vessels were found to alter dolphin behavior before, during, and after interactions and regulation breaches, including increased mating (mate guarding) and milling behavioral states, and increased ‘fish catch’, ‘high leap’ and ‘tail slap’ behavioral events. These behavioral changes may indicate masking of the dolphins' acoustic communication, disturbance of prey, increased dolphin transition behaviors, and/or induced stress and changes to group structure (including increased mate guarding). While our results provide evidence of short-term altered behavior, the potential for long-term effects on population dynamics for this threatened species is high. In the context of reported inadequate cetacean protection Australia-wide, our management recommendations include greater monitoring and enforcement, and the utilisation of adaptive management.