AbstractWe evaluated how ranges of four endemic and non-endemic aquatic ostracode species changed in response to long-term (glacial–interglacial cycles) and abrupt climate fluctuations during the last 155 kyr in the northern Neotropical region. We employed two complementary approaches, fossil records and species distribution models (SDMs). Fossil assemblages were obtained from sediment cores PI-1, PI-2, PI-6 and Petén-Itzá 22-VIII-99 from the Petén Itzá Scientific Drilling Project, Lake Petén Itzá, Guatemala. To obtain a spatially resolved pattern of (past) species distribution, a downscaling cascade is employed. SDMs were reconstructed for the last interglacial (∼120 ka), the last glacial maximum (∼22 ka) and the middle Holocene (∼6 ka). During glacial and interglacial cycles and marine isotope stages (MISs), modelled paleo-distributions and paleo-records show the nearly continuous presence of endemic and non-endemic species in the region, suggesting negligible effects of long-term climate variations on aquatic niche stability. During periods of abrupt ecological disruption such as Heinrich Stadial 1 (HS1), endemic species were resilient, remaining within their current areas of distribution. Non-endemic species, however, proved to be more sensitive. Modelled paleo-distributions suggest that the geographic range of non-endemic species changed, moving southward into Central America. Due to the uncertainties involved in the downscaling from the global numerical to the highly resolved regional geospatial statistical modelling, results can be seen as a benchmark for future studies using similar approaches. Given relatively moderate temperature decreases in Lake Petén Itzá waters (∼5 ∘C) and the persistence of some aquatic ecosystems even during periods of severe drying in HS1, our data suggest (1) the existence of micro-refugia and/or (2) continuous interaction between central metapopulations and surrounding populations, enabling aquatic taxa to survive climate fluctuations in the northern Neotropical region.