Water ferns of the Salviniaceae family are successfully used for bioremediation and bioindication of contaminated waters. Due to intensive propagation they are able to produce a great volume of biomass enriched with natural plant growth regulators. Simultaneously, water ferns have become an impediment to the use of water resources through the fast spread. Their growth and development is under control of phytohormones, which are main chemical messengers regulating the responses to environmental changes. Today hormonal system of water ferns of the Salviniaceae family remains understudied. In this review, we analyzed and summarized the literature data and the results of our own research about the role of auxins, cytokinins, gibberellic, abscisic, salicylic and jasmonic acids in regulation of growth and development of water ferns from Salvinia and Azolla genera emphasizing the specific hallmarks of these phytohormones in ferns. We have submitted brief information about methodological approaches for endogenous phytohormones determination in water ferns of the Salviniaceae family. The effects of exogenous regulators on growth, development and tolerance of water macrophytes from Salvinia and Azolla genera were discussed, as well as the possibility of using water ferns to create ecological biofertilizers.