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Marine contamination arising from land-based sources is on the rise along the Kenyan Coast. We carried out a decadal pollution survey between 2008 and 2018 to determine the levels of various pollutants (nutrients, trace metals, persistent organic pollutants, and 210 Po) in water, sediment, and biota collected from selected locations in Kenya. Nutrient levels in water ranged between <0.10 and 1560.00, <0.10 and 1320.00, and <0.10 and 3280.00 μg/L for PO 4 3−-P, (NO 2 − + NO 3 −)-N, and NH 4 +-N, respectively, while Chl-a values ranged between 0.02 and 119.37 mg/L. Total PAH, PCBs, and OCPs in sediment from the studied locations ranged from BDL-37800, 0.012-7.99 and BDL-6.10 ng/g. High level of PAH in Kilindini port was primarily from petroleum sources. DDD + DDE/DDT ratio was above 0.5 suggesting historical input. Sediment trace metal concentration from selected locations in Kenyan estuaries had various ranges, that is, Al (0.06-9804284.00 μg/g), Zn (3.82-367.20 μg/g), Cu (7.5-169.60), Cd (DL −2.40 μg/g), Mn (BDL-169.60 μg/g), Cr (2.55-239.10 μg/g), and Pb (BDL-135.60) μg/g dw. Surface sediment 210 Po activities ranged between 20.29 and 43.44 Bq kg −1 dw. Chl-a and PO 4 3−-P data revealed enhance primary productivity in Mombasa peri-urban creeks and estuarine areas. Although the reported concentrations of trace metals and POPs are low in most locations from Kenya, there is a potential risk of bioaccumulation of these contaminants in marine biota; thus, there is a need for continuous monitoring to protect both ecosystem and human health.