The Natural Park of Albufera (Valencia, Spain) is one of the Spanish Mediterranean wetlands where rice is cultivated intensively. The hydrology of the Albufera Lake, located in the center, combines natural contributions with complex human management. The aim of our study was to develop a new methodology to accurately detect the volume of flood water in complex natural environments which experience significant seasonal changes due to climate and agriculture. The study included 132 Landsat images, covering a 15-year period. The algorithm was adjusted using the NDWI index and simultaneous measurements of water levels in the rice fields. The NDVI index was applied to monitor the cultivated area during the summer. Lake inflows and residence times were also evaluated to quantify how the hydrodynamic of the lake is conditioned by the agricultural management. The algorithm developed is confirmed as a useful ecological tool to monitor the flood cycle of the wetland, being able to detect even the lowest water levels. The flood dynamics are consistent over the fifteen years, being in line with the rice cultivation cycle. Water renewal in Albufera lake is altered with respect to that expected according to the rainfall recorded in the study area, so an improvement in the water management of the hydrological basin is required to optimize the runoff during the rainiest months.