Abstract Geodiversity offers novel insights into biodiversity patterns and their underlying mechanisms, thereby contributing to the development of conservation strategies amid widespread environmental changes and human disturbances. However, the relationship between geodiversity and biodiversity remains largely unexplored, particularly in freshwater ecosystems. Here, we investigated the extent to which geodiversity accounts for fish diversity across dimensions (taxonomic, functional and phylogenetic) and levels (alpha and beta) of biodiversity in the Lancang‐Mekong River. We first compiled three freshwater fish datasets (i.e. occurrence records, functional traits and phylogenetic relations) and seven geofeature group datasets (i.e. discharge, waterbody, topography, terrestrial cover, landform, soil and rock) of the catchment. Multidimensional fish diversity and geodiversity were then calculated at alpha and beta levels, respectively. Next, we assessed the influence of geodiversity on multidimensional fish diversity at corresponding levels using generalized linear mixed models (GLMMs) and structural equation modelings (SEMs). Multidimensional fish diversity showed contrasting patterns across diversity levels, with alpha diversity showing positive upriver‐downriver gradients, but beta diversity showing negative gradients along the river continuum. The spatial congruence in geodiversity was weak across geofeatures and diversity levels. Geodiversity substantially accounted for the variance in fish diversity at both alpha and beta levels, with conditional R 2 in GLMMs ranging from 0.892 to 0.996. The increase in alpha fish diversity was primarily driven by the growing variability of discharge and waterbody types, while the increase in beta fish diversity was mainly influenced by the rising dissimilarity of discharge and soil types. SEMs revealed that the indirect effects of geodiversity on fish diversity were widespread but generally weak. Synthesis and applications . Our findings emphasize the profound influence of geodiversity on multidimensional fish diversity in large rivers, revealing its central role in shaping biodiversity through enhancing environmental heterogeneity and resource availability. To sustain fish diversity, it is crucial to maintain the variability of discharge and waterbody types and preserve linkages among geodiversity components. Integrating geodiversity into conservation programmes provides a robust framework for ensuring freshwater ecosystem resilience and functionality and guiding management and restoration globally, particularly in the face of rapid environmental changes.