One of the main efforts of Archipelagos has been to establish the first non-governmental, non-profit independent laboratory in Greece. The Archipelagos laboratory facilitates studies, which detect and analyse potential sources of pollution that are harming marine and terrestrial ecosystems, as well as the public health of inhabitants living on the islands and coastal regions of Greece and the NE Mediterranean.

For this purpose, Archipelagos laboratory is, and continues to be, gradually equipped (see Archipelagos Equipment), (partly through self-funding and partly through donations) and offers local communities free of charge, analyses of drinking water and swimming water and soil quality. Analyses are also being performed with the aim to detect pesticide residues in plant tissues, final products (e.g. wine and oil) and also in soil samples. Potential microbial contamination of vegetables is also being assessed. Other analyses carried out include assessing the pharmacological potential of marine organisms.

All of the techniques used in the Archipelagos laboratory are certified and produce scientific, reliable results. Further analyses – mainly of pollution - that require resources beyond those currently available at the Archipelagos laboratory, are undertaken at collaborating university laboratories.

The Archipelagos laboratory is located at the Archipelagos research base on Samos and a smaller lab unit operates at the Archipelagos research base on Ikaria. In addition, an “on-board” lab is also currently being developed on the Archipelagos research boat, Pinelopi. The on-board lab will facilitate water analyses in various parts of the Greek seas during Archipelagos’ research expeditions.