Assessments of the ecological condition of Chinese waterbodies have increased substantially in recent years; however, the field is still in an early developmental stage, facing challenges such as an incomplete theoretical framework, imprecise methods, and limited comparability across studies. To advance scientific progress in China by leveraging mature international experience, this review synthesizes the role of ecological theory in guiding aquatic ecological assessments and provides recommendations for its application. The theoretical foundation of these assessments lies in biota-environment relationships, with niche and community-assembly (metacommunity) theories being particularly influential in shaping assessment paradigms, optimizing indices, and improving assessment performance (i.e., the effectiveness in indicating anthropogenic disturbance). Methodologically, assessment approaches have evolved from early physico-chemistry-based evaluations to a contemporary paradigm centered on biological assessment, supported by physico-chemical measures. Diagnostic frameworks that integrate quantitative condition assessment with stressor identification now represent the prevailing approach. In developing assessment indices, there is increasing emphasis on biological functional traits as sensitive metrics, leading to the widespread adoption of multimetric indices that integrate disturbance-tolerant taxa, biodiversity, and functional traits. The performance of these methods is typically evaluated across several dimensions: precision, bias, responsiveness, sensitivity, and consistency. To enhance performance, standardized survey and analytical procedures are essential, alongside the use of anthropogenic disturbance gradients to define reference conditions and predictive models to account for natural variability. Despite these advances, the ecological foundations for setting reference conditions and ecological class criteria, as well as for stressor diagnosis, require further development. International experience underscores that robust aquatic ecological assessment must be grounded in ecological theories. For China, future efforts should prioritize accounting for natural variability, empirically selecting metrics 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, promoting a transition toward greater precision, standardization, and automation, thereby providing stronger support for aquatic ecological management and international environmental commitments.