Baseline study of natural (7Be, 210Pb, 226Ra, 234Th, 228Ra, 40K) and anthropogenic (137Cs) radionuclides was carried out in two cores collected from Sabaki River estuary (Kenya, Indian Ocean). There was no exponential decrease of excess 210Pb down the cores, which did not allow dating and determination of heavy metal pollution history. The use of 137Cs as a time marker was not possible due to its low fallout rates in East Africa. The short-lived radioisotope 7Be, a tracer of river floods, confirmed 2018 flood in Sabaki River estuary. Heavy metal concentration in the two cores showed nonsystematic trends with depth. Only Pb concentration in Sabaki River estuary was higher than the background levels. Application of the “Environmental Risk from Ionising Contaminants Assessment and management” (ERICA) tool confirmed that the potential dose rates to biota from the sediment radioactivity concentrations are unlikely to pose appreciable ecological risks.