Chemical contaminants are released from mining, domestic and industrial effluents into an aquatic environment. Sediments (n = 10) were collected with an Eckman grab at ten stations in the Densu Estuary for ecological risk assessment. The spatial distribution of organic characteristics and ecological risk of metals—zinc, lead, copper, mercury, iron, and manganese in sediment—were analyzed using standard methods. The organic parameters occurred in the ranges, as follows: % C, 0.76 to 2.05, % TN, 0.06 to 0.015; % TP, 0.44 to 1.38; and C/N, 12.31 to 34.81. The ranges of metal concentrations (mg/kg) were as follows: Fe, 201.10 to 720.90; Mn, 40.10 to 152.70; Zn, 7.3 to 158.3; Pb, 1.9 to 84.7; Cu 3.4 to 23.0; and Hg, 0.01 to 0.05. The mean concentration of metals in the sediment were Fe > Mn > Pb > Zn > Cu > Hg. The highest mean concentration of Fe suggested redox conditions in the Densu Estuary. There is a low contamination factor (CF) for five metals (Zn, Hg, Fe, Cu, and Mn) (CF < 1) to high contamination of Pb (3 < CF ≤ 6). The average Pb concentration was above local and geological backgrounds, suggesting an anthropogenic source of pollution from industrial and domestic effluents and agrochemicals. The sediment was extremely enriched by Pb (EF > 50) with a positive index of geoaccumulation (0 < Igeo ≤ 2) than other metals. There is considerable to a very high degree of contamination (DC) (3 ≤ DC ≥ 6) of metals in the sediment of Densu Estuary. The potential ecological risk index (≤ 40 PERI < 80) suggested a very low to moderate ecological risk of metal pollution. The study provides baseline knowledge on geochemical contamination in tropical estuarine systems for the development of effective chemical control strategies towards sustainable management of coastal waters.