The use of the new generation of remote sensors, such as echo sounders and Global Navigation Satellite System (GNSS) receivers with differential correction installed in a drone, allows the acquisition of high-precision data in areas of shallow water, as in the case of the channel of the Encanizadas in the Mar Menor lagoon. This high precision information is the first step to develop the methodology to monitor the bathymetry of the Mar Menor channels. The use of high spatial resolution satellite images is the solution for monitoring many hydrological changes and it is the basis of the three-dimensional (3D) numerical models used to study transport over time, environmental variability, and water ecosystem complexity.