Trace metals (Zn, Pb, Cu, Cd) speciation of surface sediments from Makupa creek, coastal Kenya were determined by sequential extraction procedure. The procedure was used to extract the trace metals in sediments geochemical phases (exchangeable, carbonates, Fe-Mn oxides, organic matter/sulphide, and residual). Trace metals analysis was done using ICP/MS. The trace metal speciation results indicated that Pb, Zn, and Cd were mainly associated with the exchangeable, carbonates and Fe-Mn oxides in most of the sampling sites. The highest concentration of the trace metals were associated with Fe-Mn oxides with Zn concentration at 362.5 μg/g, Pb, 31.5 μg/g. Copper was mostly associated with the organic matter/sulphide and carbonate at concentration of 117.5 μg/g and 69.9 μg/g respectively. Generally, trace metals in sediment from Makupa creek were mainly associated with the bioavailable fractions (BAF) and their ranges were: Pb (60%-98%), Zn (90%-99%), Cu (70%-91%). It was found therefore, that there was trace metals enrichment in sediments from Makupa from anthropogenic sources and bioavailable to biota.