The objective of this study is to assess the variation of pollution in the Thai-Laos Mekong associated with seasonal dynamics concomitant with the natural geological features and human activities that impact on the adverse quality of the river. The complex ecology of the 1500 km stretch of the Thai-Laos Mekong River has been studied in this paper to understand the relationship with the geomorphology, with the sub-tropical monsoonal climate and the impact of human activity. Sub-surface geology controls the nature and extent of the drainage basin and of the river channel. The volume flow of the river varies naturally and dynamically in phase with the rainfall; traditional models based on steady state hydraulics are inappropriate. Continuous erosion of the river banks and bed generates a sediment load of impure silt, mica, quartz and clay minerals that inhibits light penetration and limits the primary productivity of the river. The river separates two countries at different stages of development; it flows through or close to eight non-industrial conurbations (Populations 350,000-2,000,000) but is otherwise sparsely populated. The river is used for subsistence agriculture, village transport, fishing including aquaculture and as a source of domestic water. Hydroelectricity is generated from the Laos tributaries. The river is a depository for partially treated urban waste and untreated village waste, hence populations of E.coli bacteria sometimes render the water unsuitable for drinking unless treated with the highest value of 240/100 ml found at station 7 during the summer season of 2003. Furthermore the river is polluted by trace metals, notably cadmium and mercury, and by Polycyclic Aromatic Hydrocarbons (PAHs), which are particularly concentrated in the sediments. Previous work has shown that cadmium and mercury exceed the Probable Effect Level (PEL) values of Canadian Environmental Quality Guidelines and that the PAH concentrations were also greater than the Interim Sediment Quality Guidelines (ISQG). Consequently the fish stock, a vital source of protein for the local human population maybe seriously affected. As conflict between the demands of human activities will be exacerbated by the continuing development of the basin; monitoring must be continued and a better model of the river's ecology is needed to predict the impact of development.