The Mekong River is recognized as one of the largest rivers in the world, and also one of the richest areas of biodiversity since it is home to more than 800 fish species (So, et al., 2016). In addition to fish, it provides supporting services to an abundant number of crabs, snails, frogs, snakes, algae and higher plants. These are one of the main sources contributing to the livelihoods and food supply for about 70 million people who live in the Lower Mekong Basin (So, et al., 2016). Due to the development goals of the four Member Countries (MCs), the revenue from other development projects such as hydropower, irrigation, navigation and tourism has been used for poverty alleviation and enhancing standard of living of their peoples; however, these development projects may be a major risk to the river ecosystem and impact on people’s livelihoods and food security. Hence, since 2003 the governments and their line/implementing agencies have tried with serious effort to support the establishment of a monitoring system. This monitoring system will provide the necessary reports of changes in the river’s ecosystem in order for the stakeholders to take remedial action if necessary. In 2003, pilot studies were conducted to identify which biological indicators should be employed to assess the ecological health (MRC, 2009) of the river. The results of each site were compared and analysed on their biological variability the year after. The analysis confirmed that within site variability is comparatively low, and that the sampling effort used in the pilot studies was sufficient enough to characterize each site. In 2005, the study focused on testing the performance of assessment metrics developed and widely used elsewhere to describe community structure (abundance, species richness, a species diversity index, and a dominance index) when these assessment metrics are applied to data from the Mekong River system (MRC, 2005b; MRC, 2006). In a majority of these metrics the performance was limited. In 2006, the development of tolerance values was emphasised for each taxon (which included organisms identified to species, genus or family) that is specifically applicable to the Mekong River system. Furthermore, the other metrics were re-tested with a larger data set that became available. In 2007, the study focused on three biological metrics (abundance, richness and Average Tolerance Score Per Taxon (ATSPT)). Regression analyses were used to examine relationships between biological metrics and environmental variables. The results of the development of the biomonitoring survey are published in a series of MRC Technical Papers (MRC, 2005a; MRC, 2005b; MRC, 2006; MRC, 2008; MRC, 2010b). In 2008, the biomonitoring programme was transferred to the MRC Member Countries and with support from the MRCS, a national team in each Member Country conducted the sampling, identification, analysis and reporting at all sites in their own countries.