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Throughout 1800, there were no major naval battles, but the French and Spanish could never reinforce Egypt. Due to the size of the French and Spanish combined fleet, all of Lord Keith's ships were required to keep a watch on the French and Spanish at Toulon to avoid being outnumbered too heavily, with reinforcement for Egypt only coming from Britain, although substantial. The French could rely only on a few ships in the Atlantic for defence, but the Mediterranean diversion for the Royal Navy and Russia was enough. The situation would change in February 1801, as a major resupply effort would be underway.

In February 1801, a resupply effort would be launched from the Mediterranean, under the command of Admiral Bruix. Gantueume would support the efforts by diverting the British to Haiti and Britain before proceeding to the Mediterranean from Brest. The Russian and Ottomans could be safely ignored for the time being by France, with Egypt not being the destination for the former and the latter with a poor quality navy. Russia's Baltic Fleet was also used to reinforce the Mediterranean with the Black Sea Fleet and the Ottomans while the Royal Navy received support from Portuguese and former Dutch and French ships. Bruix would depart from Toulon on 1 February 1801.

The Egypt reinforcement convoy would reach Malta on 12 February 1801 and Alexandria on 24 February 1801. This would reinforce the Armee de La Orient in Egypt. On seeing the French approach Egypt, the patrolling British frigate Hebe escaped and informed the blockade squadron under Admiral Keith, who was prepared to give battle. Battle would involve 32 British and Coalition ships of the line and 8 frigates compared to the French and Spanish combined fleet of 38 ships of the line and 12 frigates. Most damaged ships safely evacuated to Toulon as of 15 July 1799 and several stragglers plus all ships evacuated from Malta being involved in the battle. The battle on 2 April 1801, known as the battle of Hyeres [1801], would result in the returning French and Spanish navies being decisively defeated and barred from resupplying Egypt.