Colombia is the country with the sixth highest amount of water reserves in the world, and 25% of its territory is covered by wetlands. However, approximately 50% of the country’s water is estimated to exhibit some type of contamination related to anthropic activities. An alternative for the treatment and the recovery of its bodies of water is the use of microalgae, unicellular, and mixotrophic microorganisms, as these bioreactors are highly adaptable to the environment, and their maintenance costs are minimal, because they feed on almost any substrate. In fact, different countries have already reported using microalgae as bioremediators for bodies of water. The use of these microphytes is efficient because they metabolize, degrade, or bioaccumulate heavy metals, pesticides, emerging pollutants, and antibiotics. In general, strategies relying on microalgae to eliminate pollutants are very similar to one another. For example, the first stage often includes a process of bioadsorption, consumption, degradation, and accumulation, wherein the microalgae use molecules generated from their own cellular metabolism. Some pilot studies focusing on the phycoremediation of marshes and other bodies of water have already been conducted in Colombia; however, more studies on process optimization, effectively leveraging the biodiversity of the existing microalgae, and better adapting microalgae to the region are still required.