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A system that measures impedance of a planar electromagnetic sensor is described in this paper. It has been used to estimate the amount of nitrate contamination in water samples with the assistance of a method based on independent component analysis. Nitrates sample in the form of ammonium nitrates (NH4NO3), each of different concentration between 5 mg and 20 mg dissolved in 1 litre of deionized water (mili-q) was used as one of the main references. A model based on independent component analysis was developed to estimate nitrate contamination. The model was tested with eight sets of mixed NH4NO3 and (NH4)2HPO4 water samples. From the results, the model can acceptably detect the presence of nitrate added in distilled water and capable of distinguishing the concentration level in the presence of other type of contamination. The system and approach presented in this paper has the potential to be used as a useful tool for water sources monitoring.