The impact of shipping operations on the level of trace metals along the Commodore Channel of the Lagos lagoon is a topic that requires careful consideration. Shipping activities can have a significant impact on the water quality of the lagoon, which in turn can affect the health of the flora and fauna that depend on it. This study attempts to assess the impact of shipping operations on the level of trace metals along the Commodore Channel of the Lagos lagoon. Concentrations of trace metals in the Lagos Lagoon specifically the Commodore channel were determined in March 2016, and the downstream variation was compared. Trace metals (Pb, Cd, Fe, Zn and Co) were determined using Atomic Absorption Spectroscopy (AAS). The concentration of trace metals were found to be beyond the permissible limits stipulated by World Health Organization (WHO) and European Union (EU). There exists an exception in the mean level of Zn (0.23±0.1107mg/L) in the harbor water which was lower than the WHO standard of 5mg/L as at the time of this study. The trace metals showed the decreasing order of Pb > Fe > Zn > Co > Cd with concentration of 1.0±0.6mg/L, 0.62±0.2mg/L. 0.23±0.1107, 0.14±0.12mg/L and 0.05±0.02mg/L respectively. The result of contamination factor showed the harbor water had very high degree of Pb and Cd contamination. This high CF can be caused by the shipping and vessel transportation route and gateway of the harbor into the country. Continuous monitoring is required to assess environmental quality and adopt suitable management techniques in order to prevent the negative impacts of shipping operations on trace metal occurrence in harbors.