This paper reviews the current state-of-the-art, limitations, critical issues, and new directions in freshwater plant ecotoxicology. We selected peer-reviewed studies using relevant databases and for each (1) publication year, (2) test plant species, (3) reference plant group (microalgae, macroalgae, bryophytes, pteridophytes, flowering plants), (4) toxicant tested (heavy metal, pharmaceutical product, hydrocarbon, pesticide, surfactant, plastic), (5) experiment site (laboratory, field), and (6) toxicant exposure duration. Although aquatic plant organisms play a key role in the functioning of freshwater ecosystems, mainly linked to their primary productivity, their use as biological models in ecotoxicological tests was limited if compared to animals. Also, toxicant effects on freshwater plants were scarcely investigated and limited to studies on microalgae (80%), or only to a certain number of recurrent species (Pseudokirchneriella subcapitata, Chlorella vulgaris, Lemna minor, Myriophyllum spicatum). The most widely tested toxicants on plants were heavy metals (74%), followed by pharmaceutical products and hydrocarbons (7%), while the most commonly utilized endpoints in tests were plant growth inhibition, variations in dry or fresh weight, morpho-structural alterations, chlorosis, and/or necrosis. The main critical issues emerged from plant-based ecotoxicological tests were the narrow range of species and endpoints considered, the lack of environmental relevance, the excessively short exposure times, and the culture media potentially reacting with toxicants. Proposals to overcome these issues are discussed.