Freshwater resources play a pivotal role in sustaining life and meeting various domestic, agricultural, economic, and industrial demands. As such, there is a significant need to monitor the water quality of these resources. Water quality index (WQI) models have gradually gained popularity since their maiden introduction in the 1960s for evaluating and classifying the water quality of aquatic ecosystems. WQIs transform complex water quality data into a single dimensionless number to enable accessible communication of the water quality status of water resource ecosystems. To screen relevant articles, the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) method was employed to include or exclude articles. A total of 17 peer-reviewed articles were used in the final paper synthesis. Among the reviewed WQIs, only the Canadian Council for Ministers of the Environment (CCME) index, Irish water quality index (IEWQI) and Hahn index were used to assess both lotic and lentic ecosystems. Furthermore, the CCME index is the only exception from rigidity because it does not specify parameters to select. Except for the West-Java WQI and the IEWQI, none of the reviewed WQI performed sensitivity and uncertainty analysis to improve the acceptability and reliability of the WQI. It has been proven that all stages of WQI development have a level of uncertainty which can be determined using statistical and machine learning tools. Extreme gradient boosting (XGB) has been reported as an effective machine learning tool to deal with uncertainties during parameter selection, the establishment of parameter weights, and determining accurate classification schemes. Considering the IEWQI model architecture and its effectiveness in coastal and transitional waters, this review recommends that future research in lotic or lentic ecosystems focus on addressing the underlying uncertainty issues associated with the WQI model in addition to the use of machine learning techniques to improve the predictive accuracy and robustness and increase the domain of application.