In the present work, the contemporary exhaust gas treatment systems (EGTS) used for SOx, PM, and NOx emission mitigation from shipping are reviewed. Specifically, after-treatment technologies such as wet scrubbers with seawater and freshwater solution with NaOH, hybrid wet scrubbers, wet scrubbers integrated in exhaust gas recirculation (EGR) installations, dry scrubbers, inert gas wet scrubbers and selective catalytic reduction (SCR) systems are analyzed. The operational principles and the construction specifications, the performance characteristics and the investment and operation of the reviewed shipping EGTS are thoroughly elaborated. The SCR technology is comparatively evaluated with alternative techniques such as LNG, internal engine modifications (IEM), direct water injection (DWI) and humid air motor (HAM) to assess the individual NOx emission reduction potential of each technology. Detailed real data for the time several cargo vessels spent in shipyards for seawater scrubber installation, and actual data for the purchase cost and the installation cost of seawater scrubbers in shipyards are demonstrated. From the examination of the constructional, operational, environmental and economic parameters of the examined EGTS, it can be concluded that the most effective SOx emission abatement system is the closed-loop wet scrubbers with NaOH solution which can practically eliminate ship SOx emissions, whereas the most effective NOx emission mitigation system is the SCR which cannot only offer compliance of a vessel with the IMO Tier III limits but can also practically eliminate ship NOx emissions.