Abstract In the Biosphere Reserve of the Maya Lowlands, the large‐scale characterisation of the current wetlands ecology and the exploitation and management of their natural resources by the ancient Maya is severely constrained by the forest. This paper presents an integrated geomatic, geoarchaeological and ecological approach, developed to overcome this obstacle in the microregion of the Naachtun Maya city. It is based on the analysis of LiDAR, and field and laboratory data. This approach has revealed the mosaic of current ecological conditions of the wetlands, thanks to the characterisation and spatial modelling of the landforms, hydrology, vegetation and soil cover. It has enabled the characterisation of numerous hydraulic and agricultural structures: 70 large reservoirs, raised fields (the largest over 1.5 km²), canals and ditches (with a cumulative length of over 300 km) and dikes. Eight morphological types of hybrid structures—hydraulic and agricultural—are described. These constructions have enabled the intensive exploitation of water and soil resources, their management and the resulting environmental risks. This study has shown that the agroecosystems of lowland areas were created as early as ~1500 B.C.E. and evolved in a polyphasic way, until a phase of radical decline around 1000 C.E. This study has made it possible to characterise the legacy of the Maya Early Anthropocene on current wetlands, as well as their important natural and cultural heritage.