This paper presents a multi-disciplinary characterisation of processes that influence sedimentation and lake water chemistry in the northern part of the Lake Malawi (or Lake Nyasa), East Africa. This characterisation is based on geophysical (heat-flow), tectonic, hydrological, hydrochemical (major elements, stable isotopes) and sedimentological (seismic profiles, core mineralogy) studies of data acquired from 1990 to 1994 during the CASIMIR project (Comparative Analysis of Sedimentary Infill Mechanisms in Rifts). Sub-surface activity is expressed through seismic and volcanic activity, as well as elevated heat-flow values, both beneath the lake and the surrounding area; hydrothermal activity is observed in the watershed however it was not clearly identified in the sub-lacustrine environment. Relatively high heat-flow values (80–90 mW/m 2) and the chemical composition of hydrothermal fluids in hot springs suggest the presence of a magmatic body at depth. The influence of Quaternary tectonic activity on sedimentary dynamics and infilling is observed not only on land but also in the lake through high-resolution seismic profiles. The main feature is a general tilting of the Kyela Plain as shown by a shift in the river course. The Quaternary stacking pattern of seven sedimentary sequences identified on a grid of high-resolution seismic reflection profiles represents a complete long-term lake-level cycle, from a lake lowstand at about 320 m below the present level to the present-day lake highstand. The North-Kiwira and Songwe River delta systems, composed of a number of stacked lobes, were developed in response to the interplay between gradual lake-level rise, tectonic movement and sediment input. The river dynamics is also recorded in a short core by a mineralogical evolution probably due to a decrease of detrital inputs from the Songwe River in response to hydroclimatic changes. Such changes are very important as this northern part of the watershed is considered as a recharge zone for the entire lake. Sedimentological patterns (from shallow depth to about 240 m water depth) and hydrochemistry are both influenced by watershed characteristics (pedology, geology, vegetation, hydrology, climate, etc.) but also by lacustrine biological processes: diatom productivity in epilimnetic water and degradation or preservation in deeper waters. Physico-chemistry and isotopic data of epi- and metalimnetic waters document the importance of the various water sources but also of evaporation and mixing processes linked to the thermo-haline stratification. Even if hydrothernal discharges have not been observed in the lake, they contribute to the lake chemistry at least through riverine inputs (Kiwira River).