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Worldwide, there are at least 12 ILTER sites with an emphasis on karst, landforms arising from the combination of high rock solubility and well-developed solutional channel porosity underground, but the study of cave ecosystems has been largely neglected. Only two ILTER sites, both in Slovenia, are primarily caves. Caves are under-represented for several reasons, but especially because of the overall difficulty of access and the lack of a clear research agenda for cave ecosystem studies. We review several aspects of long-term studies in Postojna Planina Cave System (PPCS), proposing our approach as a model for ILTER research in caves. In PPCS, analysis of short-term temperature data shows a muted daily cycle and seasonality, and analysis of long-term temperature data shows an increase, largely the result of climate change. Changes in drip rate of epikarst aquifers above the cave are correlated with rainfall but with lags and complications resulting from differences in longer term rainfall patterns. Analysis of discharge rates indicates a rapid response to precipitation not only in the Pivka River at its sinking, but also at Unica Spring, where discharge is augmented from other parts of the aquifer, including epikarst. Quantitative analysis of the obligate epikarst-dwelling copepod community shows that, unlike most cave communities, complete sampling of the fauna is possible. Finally, organic carbon levels in PPCS indicate likely carbon limitation in the system. These five factors (temperature, drip rate, river discharge, epikarst copepod fauna, and organic carbon) are the appropriate variables for capturing the essential long-term trends in cave ecosystems and their causes.