The described dataset was the result of a field effort consisting of several campaigns to assess the influence of carbon increase as a result of agroforestry treatments on soil hydrological characteristics and water fluxes at two sites in Malawi. At the sites, two experimental trials have been established which differ in age and soil characteristics, while climatic conditions are roughly comparable. At both sites we focused on control plots of maize and agroforestry treatments including Gliricidia sepium (Jacq.) Walp. as the tree component. The dataset contains soil characteristics such as texture, porosity, carbon and nitrogen concentrations, carbon density fractions, dispersible clay proportions, soil hydraulic conductivity and water retention curves. To assess the differences in water fluxes between treatments and sites, we installed soil moisture and matric potential sensors and a small weather station at the sites and monitored the fluxes over the course of about three months. The resulting time series are also part of the dataset, as well as some measurements of maize heights. The file structure of the dataset as well as details on the sites, sampling procedures, measurements and methodology are included in the data description.