Phycotoxins are natural metabolites produced by several species of microalgae. Under favourable environmental conditions such as light, nutrients, temperature and salinity, those algae species can grow exponentially and form dense aggregations. These aggregations are called “harmful algal blooms” (HAB) when harmful to the environment, aquatic life, and human health. In the last decades, anthropogenic activities such as fertilization, extensive fishing, sea travel and increased production of greenhouse gases have led to an increase in HAB events. Microalgae are on the base of the marine food web and, thus, are ingested by organisms at higher trophic levels, leading to transference and accumulation of phycotoxins along the food web, ending up in top predators like marine mammals, sea birds and even humans. In sea birds and marine mammals, several mass-mortality events have been associated with phycotoxins. In humans, different illnesses have been described due to the consumption of contaminated seafood, some of them causing severe gastrointestinal and neurological symptoms. Therefore, further investigations and constant monitoring of phycotoxin transference along the food web are necessary to protect biodiversity and secure food safety and human health. Marine mammals show great potential as sentinel species to study the presence and consequences of phycotoxin consumption as they are, in most cases, at the top of the marine food web, they have long life spans and have a wide range of distribution, including coastal ecosystems which are thought to be more affected by HAB. Moreover, they consume similar trophic resources to humans, confirming their potential as sentinels to assess the negative effects of HAB and phycotoxins on public health. The aim of this work was to examine different types of marine mammal tissues and body fluids for the presence of phycotoxins and, thus, implement an effective extraction protocol. The samples were collected opportunistically from stranded animals on the north and central Argentinian coast in 2018. Marine mammals’ tissues and body fluids are complex matrices that have proven to be difficult to extract. Therefore, different trials, including different extraction solvents and clean-up steps, among others, have been tested to improve the initial method draft based on the literature. Furthermore, toxin recovery with solid-phase extraction was carefully assessed. As a result, two final extraction protocols have been proposed for the phycotoxin analysis in marine mammals, which are supposed to assure a sufficient phycotoxin recovery if present in the marine mammal samples. However, during the method development, no phycotoxins could be measured in the analysed marine mammal samples; therefore, some previously planned trials could not be executed. In the future, more experiments should be carried out using marine mammal samples containing phycotoxins to evaluate further steps of the extraction protocols.