Several studies conducted on occurrences of evaporitic salts in various parts of the world often interpret the formation of such salts as the result of the evaporation of subsurface brines, saline lake waters and sea water-contaminated groundwater, on one hand, and the deposition of sea sprays and wind-transported salts, on the other hand. This study seeks to understand processes governing the formation of evaporitic salts in a humid tropical context and to establish a link between the occurrence of these salts and the different processes controlling the hydrogeochemical evolution of groundwater in Bugesera region, in north-eastern Burundi. Unlike previous studies, salt occurrences in the study area occur in a continental and humid tropical environment where chemical analyses of water samples from several small lakes reveal rather fresh water. While salt incrustations reported in the western Burundi occur in a sedimentary basin which is made up of a mixture of lacustrine and fluviatile sediments, the evaporitic salts in the depression of Bugesera appear in the upper layers of the weathered overburden developed on Precambrian basement rocks. These facts suggest that the lithological nature and setting of the area may not be the key factor controlling the formation of these salt deposits. X-ray diffraction (XRD) analyses performed on saline soils from two quarries in Bugesera region confirm the presence of salt minerals including particularly gypsum (CaSO4·2H2O), halite (NaCl) and thenardite (Na2SO4). Other minerals identified such as goethite, kaolinite, muscovite and quartz may be part of the soil matrix. Chemical analyses on leachates of soil samples from the 2 quarries in Bugesera region confirm their saline nature as evidenced by high TDS (1826–17,679 mg/l) and pH values (8.3–8.5). The predominance of Na+, Mg2+, Ca2+, K+, SO42−, Cl− in the chemical composition of the dissolved salts clearly reflects their mineralogical composition. This study clearly demonstrates that these evaporitic salts originate from the combination of three processes, namely the dissolution of aluminosilicate minerals which enrich groundwater in different salt-forming ions, the capillary rise which lifts the shallow groundwater and the dissolved ions up to the reach of evaporation and ultimately the evapoconcentration which precipitates the salts following well-established pathways. These findings are well supported by the results of the simulation of the evapoconcentration process with the PHREEQC hydrochemical model.