The extent of faecal contamination in soils and water is still poorly known in rural tropical areas despite its important consequences on both human health and the economy. Here we explore the sources, pathways, and spatio-temporal dynamic of contamination in rivers of a rural tropical area at different spatial and temporal scales. Concentrations of Escherichia coli (E. coli), a faecal indicator bacteria (FIB), were measured in the Nam Khan river, tributary of the Mekong river (North Lao PDR). Measurements were made from the headwaters to the main stream under contrasted hydrological conditions (i.e. during base flow and stormflow) and during the wet and dry seasons in 2011. The results show that E. coli contamination is controlled by both land use (i.e. stock of bacteria brought to the soil surface by the faeces of human and livestock) and hydrology (i.e. contribution of overland flow to the river discharge). Direct point-source contamination is of minor importance in this rural watershed, however, during high discharge the concentration of FIB frequently exceeds 5000 MPN 100 mL(-1). The E. coli module of the Seneque/Riverstrahler model was adapted to the context of the Nam Khan river, validated with field observations and used to analyse future scenarios of faecal contamination (changing demographic trends and improvements in wastewater management). We found that the risk of worsening FIB contamination was more related to the predicted future rural exodus and to wastewater management practices rather than to an increase in demographic pressure in these upland systems.