In the northern Neotropics, the contribution of highly diverse landscapes and geological history in structuring large-scale patterns of limnology and aquatic species association 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. Five species associations are closely related to limnological regions. The confinement of species associations is attributed to regional lake geochemistry. Microfossil evidence reveal that biological structure in the study area displays little alteration during the last 20ka, despite abrupt climate events such as Last Glacial Maximum and Heinrich Stadials. We deduce a linear, continuous and primary influence of geodiversity for limnological structure and geochemical properties and aquatic biological composition in the northern Neotropical region since the late Pleistocene.