This review comprehensively evaluates the impacts of anthropogenic threats on beaked whales (Ziphiidae)—a taxonomic group characterized by cryptic biology, deep dives and remote offshore habitat, which have challenged direct scientific observation. By synthesizing information published in peer-reviewed studies and grey literature, we identified available evidence of impacts across 14 threats for each Ziphiidae species. Threats were assessed based on their pathways of effects on individuals, revealing many gaps in scientific understanding of the risks faced by beaked whales. By applying a comprehensive taxon-level analysis, we found evidence that all beaked whale species are affected by multiple stressors, with climate change, entanglement and plastic pollution being the most common threats documented across beaked whale species. Threats assessed as having a serious impact on individuals included whaling, military sonar, entanglement, depredation, vessel strikes, plastics and oil spills. This review emphasizes the urgent need for targeted research to address a range of uncertainties, including cumulative and population-level impacts. Understanding the evidence and pathways of the effects of stressors on individuals can support future assessments, guide practical mitigation strategies and advance current understanding of anthropogenic impacts on rare and elusive marine species.