Chronic diseases that plague global health require further study to develop effective treatments, as they still cause high mortality rates. Alongside traditional therapies, these diseases have attracted interest for their potential to be treated with natural bioactive substances that have fewer toxic side effects. These include compounds derived from various aquatic plants with potential medicinal properties. This chapter explores the use of aquatic plants as sources of bioactive substances with antithrombotic, anti-inflammatory, and antioxidant effects. The focus shifts to well-known aquatic plants, which have established but not fully understood biofunctional and medicinal properties. It also highlights lesser-studied aquatic plants that have yet to be thoroughly researched for such applications. Many of these plants grow naturally in large numbers on the surfaces of water bodies. Their persistent growth suggests they could serve as sustainable sources of natural bioactive compounds if properly harnessed for economic gain in an environmentally friendly manner. This chapter provides detailed information on the abundant bioactive components present in freshwater aquatic plants, which exhibit strong antioxidant, anti-inflammatory, and antithrombotic activities, as well as their extraction methods. Their high levels of alkaloids, phenolic compounds, and terpenes indicate these plants are promising sources of bioactive compounds with potential applications in functional foods, cosmetics, and pharmaceuticals aimed at combating chronic diseases related to inflammation and thrombosis. Further research is needed to verify their safety and effectiveness.