The mountain complex of the Serrania de la Macarena on which the river flows is characterized by the presence of very ancient quartzite rocks dating back to about 1.2 billion years ago, extreme western extension of the Massif of Guyana in Venezuela. Being a minor waterway, the Caño Cristales does not reach 100 km in length and never exceeds 20 m in width. It is a fast flowing river with many rapids and waterfalls. In many parts of the river bed there are circular wells called giant potholes that are believed to have been formed by pebbles or pieces of rock harder than the one in which the river flows: if trapped by the current obstructed by any obstacle, these fragments of rock scrape the walls around the obstacle creating a cavity. Over time, other fragments of hard rock fall into the cavities already present and, rotated by the current of water, continue to affect the wall, increasing the size of the well.
The Serranía de la Macarena is located on the border of three large ecosystems, each with a high diversity of flora and fauna: the Andes, the eastern Llanos and the Amazonian rainforest. Plant and animal life is struggling with the lack of nutrients on the solid rocky surface of the plateau and has developed several adaptations. The representative biome of the Serranía de La Macarena is the hydrophytic rainforest: hot, warm and cold. The plateau is home to about 420 species of birds, 10 species of amphibians, 43 species of reptiles and eight of primates. The Caño Cristales has a great variety of aquatic plants. The river water is extremely clear due to the lack of nutrients and small suspended particles. Almost unique is the bright red-pink colouring of the river bed that is observed after the rainy season, at the end of June until November. This colour is caused by large quantities of endemic Macarenia clavígera plant species. This plant can only be found in a few other local rivers, such as the Caño Siete Machos. These red plants adhere firmly to the rocks where the river has a faster current.