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High mountain lakes provide essential ecosystem services and have a high conservation value. Therefore, understanding how glacier retreat will affect their ecological functioning and water quality is crucial. Here, we tested how shallow high mountain lakes having different glacial influences differ in their abiotic main features and food web structure using a multiple ecological indicator approach. We identified 13 functional groups within the planktonic and littoral communities, each one representing a biotic indicator and a node in a simplified food web network. The abiotic environment and most functional groups differed significantly as a consequence of the glacial influence. In general, runoff from glacial meltwaters resulted in highly simplified food webs. Considering that many turbid glacially fed lakes are losing their hydrological connection with disappearing/retreating glaciers and shifting to a clear state, our results suggest that this shift could enhance food web complexity, but at the cost of losing specific habitats. Further, retreat of large glaciers will form new glacially fed lakes, but it remains unclear whether this will buffer the expected habitat and biodiversity loss. [ABSTRACT FROM AUTHOR]