The EU-funded CREATING project (Concepts to reduce environmental impact and attain optimal transport performance by inland navigation -- bureaucrats probably ran out of fund when time came to find a "G" word to finish the clever acronym) along with BP have been working on creating cleaner ships for inland navigation. Currently, CO2 emissions per ton/km for inland navigation are lower than they would be with trucks, but criteria pollutants (NOx, SOx, PM, etc) are much higher.
"The project is based on four principle technologies: urea-based selective catalytic reduction; diesel particulate filters; ultra low sulfur fuel equal to road standard diesel fuel (EN 590); and the Advising Tempomaat (ATM), [a computer program advising the skipper on the most economical combination of route and speed]."
A BP ship, the Victoria, a 1,300 tonne, 70-meter vessel, was modified to demonstrate in real-world conditions these technologies at work.
These modifications are expected to cut down NOx emissions by 92% and particulate matter by 98%. In addition, SOx emissions will be almost completely eliminated, while CO2 emissions are expected to be reduced by 5%.
This impressive reduction in criteria pollutants is welcome, but very late. Basically, this is just cargo ships playing catch up with most other machinery and vehicles that are on ground.
Also, this project is just for coastal and inland navigation - where air quality has the biggest impact, but still - and we can expect high-sea ships to keep polluting as much as before for the near future.