Remote sensing allows the study of aquatic vegetation cover in shallow lakes from the different spectral responses of the water as the vegetation grows from the bottom toward the surface. In the case of Gallocanta Lake, its seasonality and shallow depth (less than 2 m) allow us to appreciate the variations in the aquatic vegetation with the apparent color. Six common vegetation indices were tested, and the one with the best response was the so-called NDI45, which uses the normalized ratio between the far red (705 nm) and red (665 nm) bands. Our aims are to show the variations in the surface area covered by vegetation at the bottom of the lagoon, its growth and disappearance when drying occurs, and recolonization in a flooding period. The degree of cover reaches 90% at the most favorable times of the year, generally in summer and coinciding with flooding of the lake. The studied period shows how this method can be used for lacustrine habitat detection and highlights the need for field vegetation inventories in future works, which will allow the spectral measurements to be related to the species present.