Tufa deposits are high-resolution archives of Quaternary environmental change, yet the interpretation of their fossil ostracod assemblages is often limited by a lack of well-calibrated modern analogues. This study addresses this gap by conducting a multi-proxy analysis and direct comparison of two tufa-depositing systems in Thuringia, Germany: the modern Pennickental stream and an early Holocene profile from Plinz. By integrating ostracod, mollusc, plant macrofossil, and sedimentological data within the established palynological and isotopic framework for the Plinz site, we reconstruct a three-stage hydrological succession. The record begins with a cool, stable, spring-fed stream during the post-glacial transition (Zone A), transitions to a shallow, standing-water pond during the climatic amelioration of the early Holocene (Zone B), and ends in a cool, groundwater-dominated mire following a late Preboreal/early Boreal cooling event. In contrast, multivariate analysis of the modern Pennickental system reveals a spatially heterogeneous community structured by contemporary hydrochemical and hydrodynamic gradients. This comparative framework allows for the decoupling of two fundamental modes of biodiversity organization: the high temporal beta diversity at Plinz, driven by long-term ecological succession and faunal turnover in response to major climatic forcing, versus the high spatial beta diversity at Pennickental, maintained by niche partitioning in a mature, stable ecosystem. Our findings indicate a “no-analogue problem” comparing the two data sets but provide a robust, multi-proxy framework for critically applying modern spatial data to the interpretation of temporally dynamic records of the past.