<p>Inland water ecosystems are sensitive to global change and anthropic pressure, especially to land conversion and modifications of the drainage network. The impacts depend on the type of environment and while the general mechanisms impacting continental wetlands are known and documented, regional studies remain compulsory to constrain the issues relative to a particular catchment. The Lake Victoria basin in Eastern Africa is a key example of the urgent necessity to conduct such regional studies. Lake Victoria is the second world largest freshwater body and its basin sustains a rapidly growing population of about 42 million people. The poorly mechanized agriculture in some of the sharing countries makes for extensive conversion of land, deforestation and soil degradation. This study addresses the interactions between lakes, rivers and the connected floodplains in the Nyabarongo – Kagera river system, in the southwestern part of Lake Victoria basin. Using remote sensing images, climate and water discharge data, this work discusses how a sudden modification in the local drainage resulting from an acceleration of natural processes by human activity such as catchment-wide deforestation and rapid conversion of the Nyabarongo River floodplain to agriculture modified the environment of Lake Rweru. In a matter of a few years, this event created a new delta, strongly affected the lake water quality and modified the water discharge and sediment load downstream the lake. The results advocate for an increased research effort to better support initiatives to preserve these valuable wetland ecosystems.</p>