These two ports were already the only ones among continental Europe's 10 biggest to report a drop in goods handling over the last decade, Eurostat data show.
While the Covid-19 pandemic has hit global ports hard, for the French ones it came on top of paralysing strikes that pushed clients such as Mediterranean Shipping Co (MSC) to rivals.
Their inability to shake off a reputation for labour unrest and inefficiency - with dockers torching tyres and blocking roads in December and January to protest pension reforms - is complicating revival efforts.
'Coming off a series of strikes into the coronavirus crisis was not the most helpful,' said Eleanor Hadland, senior analyst at London maritime consultancy, Drewry. 'Any recovery from the strikes just didn't really happen.'
With European ports starting to report first-half traffic, the combined damage of strikes and coronavirus to French harbours has become clear: tonnage handled by Seine River ports including Le Havre slumped 19 per cent, compared with drops of 4.9 per cent and 9.1 per cent for northern rivals Antwerp and Rotterdam.
French port container volume suffered with traffic falling 29 per cent in Le Havre and 17 per cent in Marseilles. Antwerp reported a 0.4 per cent increase, while Rotterdam recorded a drop of seven per cent. Marseille's Italian rival Genoa registered an 11 per cent decline.
The United Nations Conference on Trade and Development June forecast said international trade in goods may plunge 20 per cent in 2020 due to the pandemic, after falling 27 per cent in the second quarter.