Trace metals and organic pollutants are ubiquitous marine contaminants that do not readily break down in the environment, instead dispersing into various compartments including the tissues of marine biota. These contaminants biomagnify up trophic levels, leaving apex predators and long-lived marine mammals like cetaceans at risk of toxicity. Effects include reproductive, immune and neurological dysfunction, all of which have the capacity to severely affect entire populations. In the last decade, an alarming number of beaked whales (Ziphiidae) have stranded on the NSW coast. Beaked whales are extensively data deficient, as is contaminant data for cetaceans in Australia. Tissue samples from 18 stranded individuals (16 Ziphiidae specimens, one Megaptera novaeangliae, one Kogia breviceps) were collected at post-mortem, samples were processed and analysed for trace metals and organic contaminants. Results were compared between species, age class and tissue type, with post-mortem reports discussed. Highlights from this study include the first comprehensive contaminant analysis of cetaceans stranded in NSW, potentially toxic trace metal burdens in some individuals (mercury, silver, cadmium), and the presence of organic contaminants including pesticides and Polychlorinated byphenyls (PCBs) particularly in one post-flood specimen. Challenges in wild cetacean sampling, monitoring and pollutant mitigation are also discussed, as are future suggestions.