Inventories provide information on the state of biodiversity at a site or for a geographic region. Species inventories are the basis for systematic study and critical to ecology, biogeography and identification of biological indicators and key species. They also provide key information for assessments of environmental change, for natural resource conservation or recovery of degraded ecosystems. Thus, inventories play a key role in planning strategies for conservation and sustainable use. This study aimed to inventory the fauna of water beetles, larvae and adults, in two mountainous regions in the state of São Paulo, in Serra da Mantiqueira (Parque Estadual de Campos do Jordão and Pindamonhangaba region) and in Serra do Mar (Santa Virgínia and Picinguaba Divisions) as well as to generate information about the habitats used by the different genera recorded. Specimens were collected in lotic and lentic systems, between the years 2005 to 2010. In total 14,492 specimens were collected and 16 families and 50 genera of Coleoptera were identified. This study in mountainous regions showed a significant portion of the faunal composition of South America and the state of São Paulo. The composition of the fauna, in terms of richness and abundance by family, indicated the predominance of Elmidae, followed by Hydrophilidae and Dytiscidae. Despite the diversity found, the results of estimated richness indicated the need for additional sampling effort for both regions, since the curves of estimated richness did not reach an asymptote, suggesting that new species can be found in future surveys.