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Lake Prespa and Lake Ohrid, located in south-eastern Europe, are two lakes of extraordinary ecological value. Although the upstream Lake Prespa has no surface outflow, its waters reach the 160 m lower Lake Ohrid through underground hydraulic connections. Substantial conservation efforts concentrate on oligotrophic downstream Lake Ohrid, which is famous for its large number of endemic and relict species. In this paper, we present a system analytical approach to assess the role of the mesotrophic upstream Lake Prespa in the ongoing eutrophication of Lake Ohrid. Almost the entire outflow from Lake Prespa is found to flow into Lake Ohrid through karst channels. However, 65% of the transported phosphorus is retained within the aquifer. Thanks to this natural filter, Lake Prespa does not pose an immediate threat to Lake Ohrid. However, a potential future four-fold increase of the current phosphorus load from Lake Prespa would lead to a 20% increase (+0.9 mg P m−3) in the current phosphorus content of Lake Ohrid, which could jeopardize its fragile ecosystem. While being a potential future danger to Lake Ohrid, Lake Prespa itself is substantially endangered by water losses to irrigation, which have been shown to amplify its eutrophication. [ABSTRACT FROM AUTHOR]