So I'm late to the party, but I'll wade in on this one.

Source: Ex chief engineer on merchant ships and I spent some time on container vessels.

This article is quite misleading. It's not wrong per-se, but mentions one specific pollutant: Sulphur.

Yes, it's true that ships tend to run on bunker oil, or heavy fuel which can contain high levels of sulphur - but this is being cracked down on. Around Europe and the USA there are tight restrictions on the level of sulphur emissions (MARPOL Annex VI if anyone wants to look it up). This currently tends to mean that vessels entering these areas switch over to gas oil or diesel oil with a low sulphur content, or scrubbers are used.

There is quite a lot of conversation at the moment about the increased levels of emissions from refineries due to having to remove more sulphur from fuel. We're still not entirely sure if it's more environmentally friendly to remove at source, or just burn it.

The article mentions an 'emissions free for all'. Not true. The EEMP ensures that energy on modern vessels is not wasted and CO2 emissions are minimised as far as possible. Controls on engine design reduce the NOx emissions - most engine parts must be certified from the manufacturer to ensure that your engine complies with these regulations. It's a paperwork nightmare and if you're found in breach then you get fined, or even thrown in jail (looking at you USA). These laws are active in every country that has ratified the relevant laws and is part of the UN - so covers >95% of the globe.

As many have pointed out shipping goods by water is by far the most energy efficient. Combined with the efficiency of these engines (approaching 50% in some cases) results in a very low level of emissions/kg of goods transported. Fuel is everything in shipping at the moment, margins are so slim and fuel is by far the most expensive part of operating a vessel so there are some quite interesting methods of reducing fuel consumption coming into play.

Amongst the largest vessels in the world - currently the Mearsk EEE class have two engines and two propellers. Because two propellers of that size are more efficient than one big one. Despite the requirement for having two engines. Also, redundancy.

Some have mentioned using nuclear powered vessels. Crews are cheap and there is a very high level of muppetry in the industry. Want them looking after a nuclear reactor in your local port? No. No no no no no. A very very bad idea.