Deep groundwater aquifers are exploited for a variety of purposes. In general, impermeable rock layers protect these aquifers from anthropogenic influences. As such, they are a last resort for groundwater in a pre-industrial state, and a crucial resource in cases of emergency, such as floods contaminating shallow groundwater. The EU Water Framework Directive (WFD) provides the regulatory framework to protect its quality and quantity. Recent monitoring of the hydrochemical state of Upper Jurassic wells in Bavaria and Austria has shown fluctuations that were connected to new exploitation activities and might indicate an unsustainable development of the aquifer. We propose a new workflow in accordance with the WFD which uses clustering algorithms to assess these fluctuations. Our data consists of 5 to 42 hydrochemical analyses per well with yearly sampling intervals spanning up to 30 years. From the cluster analysis we derived thresholds for two corridors: Natural Range Corridor (NC) and Action Corridor (AC). While the NC represents a well-specific natural variation range, the AC hints towards unsustainable development and should trigger a detailed (re)assessment. To show the potential of the new method, the workflow was applied to two wells with different geological characteristics. Distinct fluctuation events were clearly recognized and can be used in the context of an early warning system, such that malign hydrochemical variations can be detected before they become legally problematic to well operators. Our workflow thus provides a novel, robust, and reproducible method to assess the grade of sustainability at which a well is exploited and ensures a good status of a unique and important resource.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11269-023-03529-6.