Despite significant progress, certain inflammation related to chronic disorders, including cardiovascular diseases (CVD) and cancer, still present high mortality rates. Thus, further study is needed to address such pathologies more appropriately. Apart from classic therapeutics, natural bioactives with less toxic side effects have gained attention, including those with potential pharmaceutical properties derived from several plants. Within this article, the potential utilization of freshwater aquatic plants as sources of bioactives with antithrombotic, anti-inflammatory and antioxidant properties is outlined. Emphasis is given to a well-established aquatic plant with known but not fully clarified and overviewed bio-functional and pharmaceutical properties, the Chinese lotus (Nelumbo nucifera), as well as to a so far neglected aquatic plant, Lemna minor, which has not yet been thoroughly reviewed for such applications. The latent usually grows naturally in large numbers at the surface of stored water basins of retrieved water from the last stages of wastewater treatment facilities. The continuous growth of this aquatic plant in such conditions further suggests that it can be a sustainable source of natural bioactives, if appropriately valorized, with an economic benefit and in a friendly environmental approach. The abundant content of both freshwater aquatic plants in bioactive components with potent antioxidant, anti-inflammatory and antithrombotic activities is thoroughly outlined, while their applications as functional ingredients in several functional products (functional foods, cosmetics and pharmaceuticals) are also discussed. The outlined outcomes urge further study of both aquatic plants and especially of Lemna spp. to fully elucidate their potential as alternative sustainable sources of bioactive ingredients for functional foods, supplements, nutraceuticals, nutricosmetics, cosmeceuticals, cosmetics and pharmaceutical products with health-promoting properties against inflammation and thrombosis related manifestations and their associated chronic disorders.