This paper attempts to evaluate the Malaysian water quality indexing method that has been criticized for its ineffectiveness. The indexing method is referred to as the Water Quality Index of the Department of Environment, Malaysia (DOE-WQI). This index was assessed against two other indices (River Ganga Index and Minimal Water Quality Index (WQI min )) and a modified DOE-WQI was also proposed. DOE-WQI and WQI min are physicochemical indices, whereas the River Ganga Index and modified DOE-WQI are indices with the inclusion of a microbiological parameter. The assessment was conducted based on the water quality of tropical rivers in Malaysia, with specific reference to Sarawak River and its tributaries. Water quality in terms of pH, dissolved oxygen, conductivity, turbidity, total suspended solids, biochemical oxygen demand, chemical oxygen demand, ammoniacal nitrogen, and fecal coliform count (FCC) was measured from 18 stations in December 2015, January 2016, and March 2016. Generally, the river was characterized with high FCC with the four indices significantly correlated. The results demonstrated the shortcomings of the existing DOE-WQI; the physicochemical index assigned water quality to a better class than its actual conditions without taking into consideration the FCC.