Abstract. Geodiversity is recognized as one of the most important drivers of ecosystems characteristics and biodiversity globally. However, in the northern Neotropics, the contribution of highly diverse landscapes and geological history in structuring large-scale patterns of limnology and aquatic species associations remain poorly understood. We evaluate the interaction between geodiversity, limnology and freshwater ostracode assemblages to explore drivers of aquatic ecosystem structure from southern Mexico to Nicaragua. Cluster analysis based on geological, limnological, sedimentological and mineralogical characteristics of 76 aquatic ecosystems (karst, volcanic, tectonic) reveal two main limnological regions: (1) Karst terraces from the Yucatán Peninsula and northern Guatemala, and (2) volcanic terrains of the Guatemalan highlands, El Salvador and Honduras mid-elevations, and Nicaraguan lowlands. In addition, seven limnological subregions were recognized, attesting high limnological heterogeneity. Principal Component Analysis identifies water ionic and sediment composition as most influential for aquatic ecosystem classification and given their source of formation, we recognized geology as the fundamental determinant for large-scale limnological patterns. Multiparametric analyses based on biological data revealed that species association represent disjunct faunas. For instance, five species associations are closely related to limnological regions. Structural equation modelling reveals a strong influence of limnology and elevation on the biological composition, but geodiversity resulted in the most important driver. The confinement of species associations is attributed to regional lake geochemistry. We deduce a linear, continuous and primary influence of geodiversity for limnological structure, geochemical properties and aquatic biological composition in Lakes of the northern Neotropical region.