The present study attempts to examine the comparative performance of seven different WQIs, as they were computed for Polyphytos Reservoir-Aliakmon River in Greece, based on water quality monitoring data for the period between June 2004 and May 2005. The WQIs applied were: Prati’s Index of Pollution, Bhargava’s Index, Oregon WQI, Dinius’ Index, CCME WQI, NSF WQI and the Weighted Arithmetic WQI. Significant discrepancies were observed in classification results between the different methodologies. Among others, it was concluded that NSF and Bhargava indices classify the reservoir in higher quality classes, Prati’s and Dinius indices in medium, while CCME and Oregon in lower quality categories.