This study assessed the physico-chemical status of sediments in the Agbede Wetlands with the aim to create a reference archive for the Edo North catchment and to further identify the characteristics mostly influenced by the natural and anthropogenic activities going on at the watershed. Nutrients, zinc, nickel and lead were identified to be mostly of anthropogenic origin, while alkali metals and alkaline earth metals were from both anthropogenic and natural sources. The clustering of stations 1 and 4 indicates that the sediment quality in the lentic systems was not completely excluded from the lotic system, suggesting that principal component analysis (PCA) and cluster analysis (CA) techniques are invaluable tools for identifying factors influencing the sediment quality. The mean values of the particle size distribution were in the following order across the ecosystems: sand (61.86–80.53%) > silt (9.75–30.34%) > clay (7.83–13.89%). The contamination of the water bodies was primarily derived from agricultural run-offs and through geochemical weathering of the top soils. Therefore, our analysis indicates that the concentrations of cations, anions and nutrients in the sediments of the lotic and lentic ecosystems in Agbede Wetlands are not at an alarming level.