Shifting cultivation is widely practiced in many tropical mountainous watersheds. Agricultural practices are changing with the intensification of activities and the development of industrial monocultures associated with increasing land use and the use of pesticides and fertilisers. These changes have consequences for the evolution of sediment transfers in watersheds, resulting in new vulnerabilities for the inhabitants. This article shows the evolution of structural connectivity over 5 years in the village of Houaylack-Vangven, located in northern Laos, and its potential links with agricultural diffuse pollution. To develop a structural source-to-sink model to understand sediment transfers, our method was based on open-access data and various geographical tools. Field surveys were conducted to identify areas vulnerable to erosion and sediment transfers. The sources and sinks were then located using remote sensing techniques and image interpretation to then characterise connectivity rates. Finally, the relationship between the sources and sinks was analysed by graph theory to explore the potentialities for assessing the connectivity and exposure of sediment sinks. The main results are twofold: sinks coincide with areas at risk of contamination by pesticides and fertilisers, and the structural connectivity increases with the increasing of the source surfaces (swidden plots) due to the ongoing agricultural transition.