Freshwater diversity from Desertas islands (Madeira archipelago, Portugal) is poorly known, although the islands are protected and became a Natural Reserve in 1995. To fulfil this gap, several freshwater and terrestrial habitats were sampled during two field expeditions in 2013 and 2014 to Deserta Grande island. Our aim was to perform a biodiversity assessment of the freshwater biota present in Desertas islands. Here we present the freshwater and terrestrial diatom diversity in Deserta Grande island, including some notes on their ecology and distribution. This study contributes to improve the knowledge of Madeira archipelago freshwater diversity, particular in the Desertas subarchipelago. To our knowledge, we present the first diatom data for the Desertas sub archipelago. This work resulted in a list of 61 diatom taxa for Deserta Grande, from which 57 identified to species level. From the 61 new records for Desertas sub archipelago, 30 of them were also new records for Madeira archipelago. The majority of the species are strictly associated with freshwater, but several others are typically found in brackish environments revealing the influence of sea spray in inland surface water bodies of Deserta Grande, especially at lower altitudes.