Establishing reference conditions in rivers is important to understand environmental change and protect ecosystem integrity. Ranked third globally for fish biodiversity, the Mekong River has the world’s largest inland fishery providing livelihoods, food security, and protein to the local population. It is therefore of paramount importance to maintain the water quality and biotic integrity of this ecosystem. We analyzed land use impacts on water quality constituents (TSS, TN, TP, DO, NO3−
) in the Lower Mekong Basin. We then used a best-model regression approach with anthropogenic land-use as independent variables and water quality parameters as the dependent variables, to define reference conditions in the absence of human activities (corresponding to the intercept value). From 2000–2017, the population and the percentage of crop, rice, and plantation land cover increased, while there was a decrease in upland forest and flooded forest. Agriculture, urbanization, and population density were associated with decreasing water quality health in the Lower Mekong Basin. In several sites, Thailand and Laos had higher TN, NO3−
, and NH4+
concentrations compared to reference conditions, while Cambodia had higher TP values than reference conditions, showing water quality degradation. TSS was higher than reference conditions in the dry season in Cambodia, but was lower than reference values in the wet season in Thailand and Laos. This study shows how deforestation from agriculture conversion and increasing urbanization pressure causes water quality decline in the Lower Mekong Basin, and provides a first characterization of reference water quality conditions for the Lower Mekong River and its tributaries.
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