The natural forests of the Agua de la Virgen area are sub-Andean forests described as hygrophytic or subhygrophytic (meaning they require an abundance of moisture)  and equivalent to the montane and submontane ombrophilic tropical forest of the UNESCO classification (1973) and the humid, very humid and pluvial forests of the premontane and low montane from Holdridge (1967). They correspond to premontane, primary and secondary cloud forests, where the frequency of fog tends to raise the ambient humidity and decrease the evapotranspiration.

The Reserve is made up of conserved secondary forests and in an advanced stage of growth with a canopy that reaches 15 m in height and some trees exceptionally reaching 20 m, as is the case of barbatuscos (Erythrina sp.), Guamos (Inga sp.) and Sloanea sp. In general, the forests are dominated by a bamboo called locally “reed” or “common reed grass” (Rhipidocladum racemiflorum), which is the preferred feeding site for the Recurve-billed Bushbird. The most characteristic families observed in the understory are Bromeliaceae and Rubiaceae.