Assessments of the ecological condition of Chinese waterbodies have substantially increased in recent years; however, the field remains in an early stage of development, facing challenges such as an incomplete theoretical framework, imprecise assessment methods, and limited comparability across studies. To draw upon mature international experience and promote scientific progress in our country, this review synthesizes the guiding role of ecological knowledge in aquatic ecological assessments and provides recommendations for improving their application in China. Fundamentally, biota–environment relationships form the theoretical basis of aquatic ecological assessment; in particular, niche theory and community-assembly (metacommunity) theory have exerted a decisive influence on the evolution of assessment paradigms, the optimization of assessment indices, and the improvement of assessment performance, i.e., the effectiveness of the assessment in indicating anthropogenic disturbance. Assessment approaches have progressed through several stages, evolving from early physico-chemistry - based evaluations to the current paradigm centered on biological assessment with physico-chemical indices as supporting measures. Diagnostic approaches that integrate quantitative assessment of ecological condition with identification of environmental stressors have now become the prevailing framework. In developing assessment indices, increasing emphasis has been placed on biological functional traits as sensitive metrics of environmental change. Consequently, multimetric indices that integrate disturbance-tolerant taxa, biodiversity, and functional traits have become widely adopted. The performance of assessment methods is commonly evaluated across several dimensions - precision, bias, responsiveness, sensitivity, and consistency. To improve assessment performance, unified survey and analytical procedures are essential, along with the use of anthropogenetic disturbance indicators to define reference conditions and predictive models to control for natural variability. Despite these advances, the ecological foundations underlying reference condition and ecological class criteria setting, and stressor diagnosis remain insufficiently developed. Strengthening these theoretical bases is therefore critical for further improving assessment performance. International experience indicates that aquatic ecological assessment must be firmly grounded in ecological theory. Recent efforts for assessment practices in China should prioritize accounting for the influence of natural factors, selecting metrics empirically from survey data, and implementing diagnostic frameworks that explicitly link ecological condition to causal stressors. Advancing these elements will consolidate the scientific foundation of aquatic assessment, foster its transition toward greater precision, standardization, and automation, and ultimately provide stronger scientific support for aquatic ecological management and international environmental commitments.