The African Niger Delta is among the world’s most important wetlands in which the ecological effects of intensive oil exploitation and global change are not well documented. We characterized the seasonal dynamics and pollution with total-petroleum-hydrocarbons (TPHs), heavy-metals (HMs) and nutrient-loads in relation to climate-driven variables. High TPH concentrations up to 889 mg/L and HMs up to 13.119 mg/L were found in water samples, with pronounced spatio-temporal variation throughout the year. HM pollution index and contamination factor indicate serious ecological and human health hazards, especially for Cd, Cu, Hg, and Ni. Significant differences in TPHs/HMs were observed between sites and seasons, with correlations between TPHs-HMs, and climate-variables and TPHs-HMs. Nutrient levels, turbidity, salinity, temperature, and SO42- were high and interlinked with the variability of TPHs/HMs being greatest during wet season. These findings suggest an urgent need for improved pollution control in the Niger Delta taking into account the observed spatio-temporal variation and the exacerbation of effects in light of climate change. Given the high levels of contamination, further assessments of exposure effects and bioaccumulation in biota should include future climate change scenarios and effects on humans who intensively depend on the system for drinking water, food supply and livelihood.