This article deals with the development and application of a cartographic database for a synoptic Geographic Information System (GIS). Its purpose is the storage and evaluation of the heterogeneous datasets of the interdisciplinary scientific research program MADAM (Mangrove Dynamics and Management), which aims to develop recommendations for a tailored integrated coastal management scheme for the mangrove ecosystem at Bragança (North Brazil). The article describes the integration of remote sensing data, aerial photographs, as well as point data provided by fieldwork from different scientific fields. Using various innovative processing techniques and different scale-resolution levels, an assessment of temporal–spatial changes of the mangrove peninsula and the adjacent rural socioeconomic impact area, the type of mangrove structure, as well as a land-use cover analyses was undertaken. The definition of the spatial level of detail was found to be a major issue in the development of the GIS, as well as during the processing and analysis procedures. A division between strong and weak patterns in the mangrove ecosystem could be made, which implies different management measures and sets of specific interdisciplinary studies and monitoring at hierarchical scales.