Flowing through Mongolia and Russia, the Selenga River is the main tributary to Lake Baikal, the world’s largest and deepest freshwater lake. The massive wetlands of the Selenga River Delta (SRD) on Lake Baikal perform important functions, including maintaining local and regional biodiversity and improving water quality. However, there exists a paucity of habitat and relevant ecological data for monitoring system-level changes. In this study, we characterized the rich habitat heterogeneity of the SRD using advanced 8-band multispectral satellite imagery coupled with a vegetation association algorithm and relatively extensive field surveys to analyze the spatial pattern of the system at multiple scales, from habitat-specific (e.g., Dense Floating Vascular habitats [Nymphoides sp.]) to coarser scales (e.g., Emergent Herbaceous; Aquatic Bed; Unconsolidated Bottom). We achieved an overall classification accuracy of 86.5 % for 22 wetland and aquatic habitat classes at the finest scale and greater than 91 % accuracy for broad vegetation and aquatic classes at more generalized scales. Our study provides the first detailed multi-scale characterization of the SRD for the conservation and management of the system and establishes baseline information for future change detection analyses.