We report the results of a faunistic survey focused on freshwater and limno-terrestrial meiofauna to improve biodiversity knowledge in a protected area in the Eastern part of the French Pyrénées: the Massane Forest Reserve (336 ha). The survey provided 1187 occurrence records from 315 taxa (most resolved at species level), uploaded as a shared online dataset and made freely available in the Global Biodiversity Information Facility (GBIF). The highest number of occurrences and distinguishable species belong to Nematoda (775 occurrences, 172 taxa), followed by Rotifera (219 occurrences, 67 taxa), Platyhelminthes (85 occurrences, 32 taxa), Tardigrada (69 occurrences, 25 taxa), and Gastrotricha (39 occurrences, 19 taxa). A diversity of meiofaunal organisms was found, in large numbers, in all the screened samples: from stream biofilms and sediments to forest floor soils, mosses, and litter, to a broad range of tree-related micro-habitats associated with beech epixylic mosses and lichens, tree cavities, woodpecker breeding holes, bark pockets and fruiting bodies of saproxylic fungi. This survey makes the Massane forest one of the few protected areas of the world with an all-taxa biodiversity inventory including meiofaunal groups, which could serve as a standard to further consider those cryptic groups of tiny animals in forest conservation efforts.