Global Evolution and Methodological Trends in River and Lake Health Research (1991–2024): A Bibliometric and Systematic Review

River and lake health assessment has evolved from a purely ecological concept to a multidimensional framework integrating ecosystem integrity and social service functions. Based on a comprehensive dataset of 1412 papers (1991–2024), this study combines bibliometric mapping with a systematic review to track the evolution of biological monitoring and assessment methodologies. Quantitative analysis of keywords reveals that while traditional focuses on heavy metals, fish, and sediments remain dominant, there is a significant shift towards integrated frameworks where biological indicators (e.g., benthic macroinvertebrate integrity and fish retention) are increasingly coupled with social services. We critically review three assessment paradigms: single-factor bio-indicators, biological predictive models such as RIVPACS and AUSRIVAS, and multi-factor comprehensive models. The study identifies critical gaps in ecological connectivity and the management of transboundary lakes under climate change. Consequently, we propose a strategic roadmap leveraging the National Ecological Connectivity Optimization Platform and mandatory “health audits” for transboundary waters to ensure the long-term sustainability of aquatic biodiversity. This review provides a scientific basis for balancing biodiversity conservation with sustainable water resource utilization.