In the paper, we focus primarily on methodological and applied issues of information system development for operating geobotanical and spatial data, automating the process of natural resources management and mapping in order to monitor various ecosystem dynamics. The ontology of Landscape Ecology and Vegetation Science domains was studied by carrying out a structural and semantical analysis of geobotanical and spatial data. The unified conceptual model of geobotanical and spatial data was created. On this basis, we implemented a database describing current vegetation patterns and land cover. The information system for geobotanical and spatial data management was developed using present-day object-oriented methods and functional modeling. We successfully solved the complex problem of integration Google Maps and Google Earth services with the information system developed. It required applying the service-oriented approach and developing the local geoserver algorithm to adapt Google Maps and Google Earth cartographic modules to modeling and mapping vegetation and landscapes. The system enables storing a considerable amount of interconnected geobotanical and spatial data. It provides rich functional capabilities for studying, mapping, modeling and estimating the vegetation cover and environment state. The system allows even non-GIS professionals to estimate the environmental conditions; assists in image processing for landscape textures and forest digital maps based on remote sensing data. It supports 2D and 3D modeling of interactive landscape maps and succeeds in quantitative spatial analysis of semi-structured data.