Ethnogeology, the scientific study of geological knowledge of groups such as indigenous peoples, can be combined with mainstream geological sciences to enhance our understanding of Earth systems. The Amazon rain forest has been extensively studied by both mainstream scientists and indigenous researchers. We argue that knowledge of Amazonian geology and hydrology held by indigenous Uitoto experts is valid, empirically based, and, in many cases, more nuanced than mainstream scientific knowledge. We also argue that knowledge sharing between mainstream and indigenous researchers can improve geological and environmental knowledge on both sides and provide solutions for current environmental problems such as increased pressure on water resources and global warming. We applied methods from ethnography and earth science to examine the traditional ecological knowledge of an Amazonian tribe in Colombia, the Uitoto, about water, and how that knowledge correlates with that of mainstream earth scientists. The study demonstrates how ethnogeology can be applied in a water-rich environment to: (1) compare knowledge about the natural history of an area, (2) study the geological resources available and their uses, and (3) examine the bases of native classification schemes using mainstream science methods. We found parallels and complementary concepts in the two bodies of knowledge. Our results suggest that the Uitoto have a meticulous taxonomy for water and wetlands—knowledge that is essential for protecting, conserving, and managing their water resources.