This paper presents a comparison of prediction methods for a water quality index (WQI) that is used for classification of water quality in rivers or canals. In this work, we consider the water quality index of two canals namely Phadung Krung Kasem Canal and Saen Saep Canal, Bangkok, Thailand as a case study. We compare results from M5P, M5Rules, REPTree with results from multilayer perceptron. The models employ five input variables including dissolved oxygen (DO), biological oxygen demand (BOD), ammonia nitrogen (NH3-N), Fecal Coliform bacteria (FCB) and Total Coliform bacteria (TCB) which were measured in the canals. The data in this research had been collected from Bangkok Metropolitan Authority, Thailand from 1 January 2007 to 31 November 2017. The total number of data is 2,000 records. The 10-fold cross validation method is used for evaluation of prediction models. It allows to determine the most effective method. Our experimental results show that the REPTree method yielded the highest accuracy to predict water quality index compared to other methods proposed in this paper.