The epikarstic waters of a restricted sector of the Ojo Guareña cave (north Iberian Peninsula) were investigated to characterize the physico-chemical variation in an annual cycle, to improve the scarce knowledge of the aquatic cave fauna on the Iberian Peninsula, to look for distribution patterns of species per habitat along the annual cycle, and to search for the environmental basis (either physico- or hydro-geochemical) that could explain species distribution in the epikarst. The habitats studied included all puddles and gours present in the sector selected making a total of 51 chemical and 42 biological samples for the entire cycle. The waters show no appreciable contaminationand exhibit small chemical variations throughout the year which are patently affected by external weather conditions. The 53 taxa found belong to ten higher taxonomic groups (Oligochaeta, Turbellaria, Mollusca, Copepoda, Ostracoda, Isopoda, Bathynellacea, Tardigrada, Acarina and Cnidaria), and consist mainly of crustacea with a total of 27 species. Fourteen species were stygobionts (belonging to ten genera), nine of which are new to science and ten of which are endemic. Cave pools that appeared to be more stable in terms of water volume and mineralization, had a lower pCO2 and were carbonate oversaturated, harboured the greatest number of taxa. It is these pools that can maintain strictly cave dwelling species. Pools with lower levels of mineralization and greater water volume fluctuations had a lower diversity of fauna and in general lacked stygobiotic species.