Peruvian freshwater fishes and their habitats were investigated by the Natural History Museum of San Marcos University (MHNSM) as part of a long-term project. Fishes were inventoried by sampling in main drainage basins, including coastal rivers, highland rivers, and Peru's Amazonian waters. To date, the MHNSM fish collection has approximately 300,000 specimens comprising 1000 valid species in 168 families and 8 orders. The greatest diversity lies within the Ostariophysi (80% of all species) with the dominant orders being Characiformes and Siluriformes. Characidae is the most diverse family with 22.5% of all species. Protected areas (i.e. Parks, Reserved Zones or National Reserves) have been sampled intensively providing a reasonable estimates of their fish diversity. However, our knowledge is still poor for less accessible areas. More fieldwork is needed in all of the large river basins before we can have a fuller understanding of total fish diversity. As an example of ongoing efforts, we discuss specific fish inventories in both Peruvian coastal rivers and highlands and in river systems shared with neighboring countries. In addition to Peruvian fish diversity; we discuss the state of aquatic resources and habitats in Peru's principal river basins, and current problems facing such aquatic systems (e.g. inland fisheries and extractive activities such as deforestation and gold mining). Near large cities, such as Iquitos and Pucallpa, fishing effort has increased considerably in the last decade, whereas catch per unit effort appears to have decreased considerably indicating that over-fishing has become locally problematic. An overview is presented of main conservation problems, including exotic species that confront aquatic ecosystems in Peru. Finally, an environmental education program is recommended to inform the general public about the value of freshwater fishes and aquatic ecosystems and the main problems such resources are facing.