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In Europe and probably elsewhere, due to low water levels in major rivers resulting in ships running aground.

https://www.bbc.co.uk/news/business-64553079 (https://www.bbc.co.uk/news/business-64553079)

Rail is generally faster but also more expensive and consumes more energy than a ship.

I was surprised by the figure given that rail and river produce similar amounts of CO2 per tonne-km, implying similar fuel use. I would have expected river to be more efficient, but I suppose I was thinking of sea, where each ship obviously carries more than one train, as opposed to river.

Ships almost always use less fuel per ton of freight than do trains.

Total fuel used is however not the same as carbon emissions. Almost all ships use diesel fuel, which is carbon intensive. Continental railways are largely electrified, in which case the carbon emissions of an electric train will depend on how the electricity is generated. If largely from renewables then the carbon emissions will be very low.

Total costs are rather variable and depend on staff numbers, wage rates, and taxes and subsidies, not just fuel.

If part of the journey must be by rail, then making the entire journey by rail saves the costs of transhipment.
For high value goods, less capital is tied up in goods in transit.

Ocean-going ships use bunker fuel rather than diesel, but river craft might use diesel. Bunker fuel is very dirty and has to undergo on-board processing in order to make it sufficiently liquid to ignite.

Yes, you are correct, bunker oil or similar heavier grades of oil fuel have a similar carbon intensity to diesel fuel, a bit worse in fact.
So my statement that ships almost always use less fuel than trains, but on average have worse carbon emissions than an electric train still stands.

Steam ships are now largely obsolete. Modern ships use large low speed diesels. Generally run on ordinary diesel fuel in port or when first started. Changed over to heavy oil when running. The heavy oil is strained, heated and then fine filtered before use.