This dataset was created to provide an overview on the seasonal dynamics of contaminants in the Niger Delta Africa and their relationship to parameters that are likely be affected by future climatic changes. Therfore surface water samples were collected monthly from the three major ecosystem types of the Niger Delta, the Bonny estuary, the Imo river and the Lagos lagoon in the year 2021 (January to December). We sampled 3-4 stations at each of the sites, representing upper, middle, lower reaches16 (> 5 km apart). We determined analytically the concentrations of total petroleum hydrocarbons (TPHs) and heavy metals (HMs: Mn, Al, Co, B, Zn, Cr, Cu, Ni, Pb, Cd, Hg) , measured in µg/L. Other abiotic parameters such as temperature (°C), salinity (ppt), conductivity (mS/cm), DO (mg/L), TDS (mg/L), pH, were measured in-situ using a Horiba U–52 Multi-parameter meter, while, nutrients PO43- (mg/L), NO3- (mg/L), NH4+ (mg/L), and SO42- (mg/L), turbidity (NTU)) were determined using established standard methods.