Aquatic plants are a priority biological group to study due to their high representativeness in ecosystem services and because they also indicate the state of conservation of lake systems. The goal of the study is to develop an Index of Macrophytes from continental Ecuador (IMAE), which can also be applied in the Andean region as a bioindicator, thus assessing the ecological health of the continental lakes and lagoons from 12 to 4000 m, evaluating the structure and floristic composition of aquatic plants and identifying the habitat preferences of the species according to the concentration of nutrients (nitrites, phosphates and ammonium), as determining elements of their presence. 104 species of aquatic plants were found. The tolerance and indicator values have been calculated for each species meanwhile seven levels of coverage were established. Last, four classes of trophic status or water quality were defined to asses lentic systems. The present study will significantly strengthen the environmental control tools for Ecuador.