The data set contains grain size distributions, organic matter (OM) content and trace metal distribution (including Fe, Zn, Cu, Cr and Pb) of 37 shallow cores of sediments sampled from dams across the Limpopo River Basin. The dams include: Gaborone, Lotsane and Shashe dams in Botswana; Houtrivier, Nwanedi and Mutshedzi dams in South Africa; Ripple Creek and Zhovhe dams in Zimbabwe; and Massingir Dam in Mozambique. Data from two cores sampled from an oxbow lake in Mozambique are also included. The cores were collected with a gravity corer using PVC pipes of 5 cm diameter by a team from Botswana International University of Science and Technology (BIUST) led by Dr. Franchi between July 2018 and April 2021.