Freshwater ecosystems are vital for biodiversity and provide important services, but they are facing challenges in the tropical regions. Researchers have studied various aspects of freshwater science in the Tropical Anthropocene, including monitoring water quality using aquatic macroinvertebrates, assessing the impact of introduced fish and microplastics on aquatic ecosystems, and using DNA barcoding to track changes in freshwater biodiversity. The findings suggest that biomonitoring is a valuable tool for assessing changes in freshwater systems, and environmental DNA shows promise for studying biodiversity in the Neotropics. Additionally, microplastics are a growing concern for tropical freshwater ecosystems, affecting the traits of fish and invertebrates.