The state of Hidalgo (Mexico) is an important region from the point of view of biodiversity. However, there exists a significant gap in accessible knowledge about species diversity and distribution, especially regarding to freshwater ecosystems. This dataset comprises the sampling records of two projects developed in Hidalgo between 2007 and 2009 about the freshwater fish communities of Tecocomulco lake and rivers belonging to the Metztitlan Canyon Biosphere Reserve. It contains the taxonomic identity (species level) and basic biometric data (total length and weight) as well as date of collection and coordinates of more than 9000 specimens. This dataset is the primary result of the first and unrepeated exhaustive freshwater fish's survey of Metztitlan Canyon Biosphere Reserve and Tecocomulco lake. It incorporates seven more species to the regional fish fauna, and new exclusive biometric data of ten species. This dataset can be used by studies dealing with, among other interests, North American freshwater fish diversity (species richness, distribution patterns) and biometric analyses, useful for the management and conservation of these areas. The complete dataset is also provided in Darwin Core Archive format.