The Mekong River Basin (MRB) and its tributaries play an important role in the biodiversity, livelihoods, and ecological services for millions of people in Southeast Asia. In recent decades, economic development, expanded urbanization, hydropower establishment, and climate change have significantly impacted river health. This review highlights the current knowledge of the Ecological River Health Assessment (ERHA) using bioindicators, including algae, nematodes, zooplankton, macroinvertebrates, and fish, to assess water quality and ecosystem health of the MRB. We identify key challenges and propose future directions for the sustainable management of the MRB. The results highlighted that the ecological condition of the MRB varied from poor to good levels with a decreasing trend downstream. Each biological group offers distinct advantages in ERHA within the MRB. Microalgae and zooplankton are effective indicators for short-term variations, while nematodes and macroinvertebrates are reliable indicators of sediment conditions. Macroinvertebrates are best for long-term indicators, and fish reflect broader ecosystem health. Biomonitoring methodologies have advanced to incorporate multimetric indices (MMIs) and bioindicators, but challenges remain in ensuring data consistency, taxonomic accuracy, and methodological standardization. Future research should aim to standardize sampling techniques, establish consistent reference materials, and improve data processing methods, which will improve the results for the Mekong River system.