The changes in water quality owing to recirculation of water in mineral processing plants can compromise the plant performance as well as maintenance needs. Therefore, mining process water quality assessment is becoming critical. Nevertheless, very few studies have investigated the suitability of the current analysis methodology practiced in certified laboratories for evaluating mining process water quality. This article presents two case studies to highlight the major issues encountered when performing sampling for physicochemical and chemical parameters in process water at two European mine sites using procedures from two certified laboratories. In addition, microorganisms were shown to be abundant in process waters and likely affect the mining water chemistries. However, the protocols used for microbial studies are not optimal for mining process samples, and need to be improved. The results showed difficulties in providing satisfactory results when analyzing control samples. Additionally, the analysis results presented a strong imbalance in TDS and sulfur compounds. Several potential causes associated with the poor quality of the analysis results have been outlined with a specific focus on the preservation methods. A literature review on the degradation of thiosalts suggested that the current preservation procedures are not suitable for preserving sulfur compounds. Moreover, the results indicated that the water matrix strongly influenced the validity of the chosen analysis method. In conclusion, the analysis methods should be customized for the different mining water matrix types in order to ensure the accuracy and reproducibility of the results.