Purpose Trace metals accumulate in the food web and can pose high risks to human health and aquatic biota. We investigated seasonal and spatial variations of Cu, Zn, Pb, Co, and Ni mobility in surface sediments (0-5 cm) and their potential toxicity. Materials and methods The sampling was carried out in three embayments of the Ebrie Lagoon (Côte d'Ivoire) during the rainy and dry seasons. The sequential and kinetic extraction methods were used to assess Cu, Zn, Pb, Co, and Ni mobility and their potential toxicity. Analysis of variance (ANOVA) was performed to ascertain spatial and seasonal differences. Results and discussion The results showed that contrarily to Co, distribution patterns of Zn and Cu in the sediment fractions showed no spatial and seasonal variability. On the other hand, Pb and Ni distribution patterns varied highly across the bays but not seasonally. Nevertheless, repeated measurements over a long period of time should be carried out to better understand the seasonal variability of metal distribution in sediment phases. Cu, Pb, Co, and Ni were abundant in residual fraction (56.93-71.66%) in the bays. On the contrary, a very high portion of Zn (up to 70%) could be remobilized. Cu, Pb, Co, and Ni formed mainly inert complexes in sediments, while Zn formed labile complexes. Zn could pose high risk to biota, Co and Ni a medium risk, and Cu and Pb a low risk. Conclusions A combination of both sequential and kinetic methods revealed that both Zn and Pb formed labile complexes in the exchangeable and iron/manganese oxide fractions. Sequential extraction showed high Pb concentrations in the iron/manganese oxides. Thus, Zn and Pb may be highly available, which confirmed fish Pb concentrations exceeding WHO safe limits found by previous studies. Therefore, potential mobility of metals could be better assessed by the exchangeable and iron/manganese oxide fractions obtained by sequential extraction methods.