The concentrations of major, trace (TE), and rare earth (REE) elements and their seasonal and spatial distribution were studied on the fine fraction (<63 µm) of the sediments of the Lomé lagoons (West Lake, East Lake, and Lake Bè). The sediments were collected on a total of nine sampling sites (three per Lake) during two campaigns (dry season and rainy season). The quality of the sediments was assessed on the basis of the enrichment factor (EF) and the labile or non-residual fraction (NRF) in relation to the values recommended for the quality of the sediments (Sediment Quality Guidelines, SQG). The distribution of rare earth elements shows enrichments in light rare earths superior to those of heavy rare earth elements during any season. Positive Ce anomalies are less noticeable and less variable between seasons than Eu anomalies. La/Yb ratios are positively correlated with the percentage of Al and Fe oxides and with the percentage of fine fractions. The main bearing phases of rare earth elements are, therefore, Al and Fe oxides and the finest fractions of the sediments. The concentrations of trace elements vary little, according to the seasons, but show strong variations from one element to another. The degrees of enrichment obtained are moderate for Bi, Cr, Ga, Mo, Pb, Sn, and Zn (1.5 < EF < 5) to significant for As, Cd, and Sb (5 < EF < 20) for all sites of Lake Bè. For the sites of West Lake, the degrees of enrichment obtained are moderate for As, Cd, Cu, Mo, and Pb (1.5 < EF < 5) to a significance for As, Bi, Cd, Pb, Sb, Sn, and Zn (5 < EF < 20). Only the East Lake sites show high degrees of enrichment for elements such as Sb and Sn (20 < EF < 40). Trace elements (TE) such as As, Cd, Cu, and Ni have total concentrations within the range of variation of the SQG concentrations (particularly Probable Effect Level (PEL) and Effect Range Median (ERM)), whereas Cr, Pb, and Zn total concentrations are higher. The ranking of priority sites with respect to the sediment contamination is determined according to ERM and PEL quotients in relation to the probability of toxicity for benthic organisms. For almost all the sites, the priority is lowest to medium-low with regard to As, Cd, and Cu and medium-high (Cr and Ni) to highest (Pb and Zn), particularly for the East and West Lakes. Moreover, the NRF can represent significant percentages of the total TE concentrations: 5% to 15% for As, Bi, Ni, V, Mo, and Sc, 15% to 25% for Co, Cu, and Sr, 25% to 40% for Pb and Zn and, lastly, 47% to 55% for Cd.