Degradation of surface water quality is a global problem, posing significant ecological, social, and economic risks with visible long-term effects. In this context, sustainable water resource management has become a strategic challenge that requires the development and use of appropriate tools for water quality assessment and aquatic ecosystem monitoring. In this study, a bibliometric analysis of the most important water quality indicators was conducted, such as the Water Quality Index (WQI), Canadian Council of Ministers' Water Quality Index (CCME-WQI), and Oregon Water Quality Index (OWQI), along with specialized indicators, such as the Trophic Status Index (TSI) and Heavy Metal Pollution Index (HPI). In addition, this study looks at complementary assessment methods, including multivariate statistical analysis, biological assessment, ecological risk assessment methods, remote sensing, geographic information systems (GIS), and mathematical modelling. These were critically evaluated through SWOT analysis, with particular attention paid to the relationship between the assessment indices and assessment models. The results highlight the limitations of some quality indices, such as the WQI, TSI, and HPI, particularly in terms of inflexibility, ambiguity, and lack of sensitivity to certain critical parameters, which can lead to inaccurate estimates of the state of the aquatic environment. In contrast to indices with rigid formulas, CCME-WQI offers a flexible approach that reduces the sensitivity of results to the fixed structure of parameters, an advantage highlighted in the SWOT analysis. The CCME-WQI demonstrates greater adaptability, providing a better response to parameter selection and weighting, an advantage highlighted in the SWOT analysis. It has also been found that objective mathematical approaches have the potential to reduce the uncertainty associated with these indices. The effective application of surface water quality indices and assessment methods depends on coherent and continuous monitoring programs, which are often affected by institutional fragmentation and economic constraints both locally and globally.