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Due to increasing demands for irrigation using groundwater as a source there is an urgent need for efficient methods that shed light on the resulting anthropogenic impacts on the connected aquifers. Thus an innovative approach is introduced, that aims to identify predominant geochemical changes in the groundwater system. The approach involves a principal component analysis as a promising tool to disentangle the effects of different impacts and even to give a quantitative assessment of the respective effect strength at each site. The study was applied in an irrigation region of the Nuthe River Basin, State Brandenburg, Northeast Germany. The results identify the negative impacts on the groundwater quality in the aquifer used for irrigation. A decrease of shallow groundwater quality under irrigation due to contamination with fertilizers (NO3, Cl, K, Na) and a slight shift in the redox system is indicated. Beside this direct impact on the shallow groundwater a long-term impact on a deeper groundwater resource could be identified. There is clear evidence, that the contamination is not restricted to the shallow groundwater but that extraction from deeper wells increasingly includes deeper, uncontaminated groundwater resources into the local irrigation cycle. The approach can be used as a basic tool for the adaptation of sustainable agricultural irrigation management strategies.