The Brazilian Cerrado, one of the world’s 34 biodiversity hotspots, is today under increasing pressure from the intensification of agriculture, with the replacement of traditional extensive pastures by arable crops. Manmade ponds are currently widespread in rural areas of the Cerrado and provide many ecosystem services such as cattle watering, fish production, irrigation and erosion protection. As in other parts of the world, ponds are also likely to play a critical role in the conservation of freshwater biodiversity, although in the Cerrado there is still very little known about their biota. Good water quality, in particular the level of eutrophication, is a key factor in maintaining aquatic biodiversity at the regional scale. Therefore, we aimed here to assess the water quality of ponds in the Cerrado. We also assessed whether the main types of socioeconomic pond uses have an impact on their water quality. We focused on measures of primary production and conducted socioeconomic inquiries for 56 waterbodies in the Goia ˆnia Cerrado region (GO, Brazil) at the beginning of the 2012 dry season. Overall, differences in water quality appeared to be linked to the type of pond use. The trophic level, as indicated by the chlorophyll concentration and conductivity, was greater in fish ponds and seemed to be related to management practices such as fish feeding and the type of water supply, in particular relatively low inflow volume. This contrasted with ponds used for cattle watering in extensive agricultural landscapes characterized by a low trophic level potentially beneficial for regional biodiversity. Good water quality in pasture ponds may be maintained by spring water inflow or heavy precipitation. Overall, the water quality of the Cerrado ponds was good compared with the same type of waterbodies in other regions of the world. These results highlight the high potential of the Cerrado ponds in extensive agricultural landscapes to provide an important habitat for aquatic biodiversity. Biodiversity inventories and assessments are now needed to increase our knowledge of these waterbodies and inform management activities at the local and regional scale.