Understanding the levels and associated ecological risk caused by heavy metals is important for the sustainable management and utilization of Lake Chilwa catchment, an important ecosystem in Malawi providing fertile lands for agriculture and a designated wetland ratified by the Ramsar convention in 1997. Concentrations of chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), zinc (Zn), arsenic (As), mercury (Hg) and cadmium (Cd) were analyzed from 22 soil sampling locations. Extraction and quantification were achieved by microwave digestion and Inductively Coupled Plasma Optical Emission Spectrometer, respectively. Mean values were detected in the following order; Zn > Cr > Ni > Cu > Pb > As. Strong correlations were observed between As and Pb (r = 0.85), Cr and Ni (r = 0.82), Cu and Ni (r = 0.81), Cr and Cu (r = 0.8), and Pb and Zn (r = 0.73) suggesting similar sources of input. Principal component analysis revealed that Cu, Pb, Zn and As originate from anthropogenic activities, while Cr and Ni were geogenic. The ecological risk caused by these metals, calculated by the Ecological Risk Index (RI) method, showed a low to moderate ecological risk. The wetland areas had higher overall concentrations and RI values compared to the rest of the catchment. It is therefore important to enforce measures to manage and control these levels to avoid their damaging effects.