Submerged sea caves are priority areas for conservation according to the Habitat Directive 92/43/CEE because of their unique biodiversity. A limited number of publications exist about communities living on sediments inside caves, mostly focused on the macrofaunal fraction (>0.5-mm body size). Meiofaunal communities (0.062–0.5-mm body size) have been largely neglected in ecological studies about communities inhabiting sea caves. In the present study, we analysed meiofaunal communities from Los Cerebros cave, a shallow marine cave (3–8 m in depth, 80 m long), with secondary openings in the inner parts and freshwater infiltrations. Sediment samples were taken by scuba divers using cylinders (cores), with known inner diameter. Sampling stations were sampled from the different sections of the cave (entrance, twilight zone, dark zone and jameos). Five surveys were carried out, from June 2003 to February 2005. Nematodes, copepods, and polychaetes dominated overwhelmingly the meiofaunal composition, with the remaining taxonomic groups being scarce. Generalized linear models showed that the high spatial and temporal variability observed among on the abundance of major meiofaunal groups inside the cave was better explained by the surveys, the section of the caves and the presence of freshwater. Higher abundances are observed near the entrance and in the station with regular freshwater input. Nematodes and polychaetes were clearly dominated by species extensively recorded in shallow subtidal sandy sediments on the study area.