Low relief oceanic islands often suffer from scarcity of freshwater resources. Remote sensing has proved to be an effective tool to generate valuable data for hydrological analysis and has improved the management of ecosystems and water. However, remotely sensed data are often tested over areas with existing validation databases and not always where the need is greatest. In this paper we address the need for topographical data to understand the hydrological system of Santa Cruz Island (Galapagos archipelago) so that management of freshwater ecosystems and resources can take place. No high resolution, high accuracy topographical data exist for Santa Cruz Island, and its growing population has created an urgent need for water resource management and protection of unique and pristine ecosystems. Inaccessible National Park land covers more than 97% of Galapagos territory, which makes the use of remote sensing methods indispensable. SRTM data was insufficient in terms of grid size (90 m) to carry out the needed data analysis. We used ASAR data (ENVISAT) in VV polarization image mode for Digital Elevation Model (DEM) generation, in order to extract drainage network, watersheds, and flow characteristics from a morpho-structural analysis. Results show the high potential of these data for both interferometric and radargrammetric generation methods. Although interferometry suffered from low coherence over highly vegetated areas, it showed high precision over the rest of the island. Radargrammetry gave consistent results over the entire island, and details were enhanced by integrating the 90 m SRTM data as an external DEM. Accuracy of the SRTM and the combined radargrammetric/SRTM DEM was similar, with the radargrammetric having a finer pixel-based resolution (20 m). Validation of the extracted drainage networks and watersheds was carried out using ground-based field observations and comparison to mapped river networks visually extracted from aerial photographs and high resolution (1 m) satellite imagery available on GoogleEarth(C). For the first time, watershed characteristics and flow paths were made available for an island of the Galapagos archipelago. Furthermore, the drainage network is shown to be strongly influenced by observed and extracted structural discontinuities. Having characterized freshwater flow, water balance calculations were carried out for Pelican Bay watershed, where urban areas, agricultural land and Galapagos National Park land are concomitant.