In 1787 a new Russian-Turkish War broke out before the young Black Sea Fleet could reach full strength. Count Potemkin could only mobilize five ships of the line and fourteen frigates against 29 Turkish ships of the line and 39 frigates. Although the commander later ordered frigates to be classified as ships of the line, in actuality the Russian force remained at a disadvantage.

Hope for reinforcements from the Baltic Fleet was quickly dashed. As in 1769, as Catherine was preparing to dispatch fifteen ships from the Baltic to join the fight in the Mediterranean. The Swedes suddenly attacked, and this ended all possibility of aid to the Black Sea since these northern-based warships could not leave the capital unprotected. The first campaign of the Black Sea Fleet in the autumn of 1787 was disastrous. A ferocious storm scattered the fleet. The frigate Crimea sank with all aboard, and the 66-gun Maria Magdalena drifted into the Bosporus, where she became easy prey for enemy ships. Potemkin reported to the Empress: "God punishes, not the Turks!" Due only to the courage and skill of the crew, the surviving vessels were able to return to Sevastopol.

While the Russians were struggling with the elements, the Turks concentrated 42 vessels in the Dnieper Firth, where the army of Potemkin was on the offensive. The only sea-borne opposition to the enemy was the Liman flotilla of Rear Admiral Nikolay Mordvinov. However, Mordvinov was not quick enough to attack the Turkish fleet, and the enemy had sufficient time to move 5,000 troops onto the Kinburn spit. Defending the fortress of Kinburn, the troops of General-in-Chief Count Alexander Suvorov, rejoined the battle. Suvorov's troops were supported by only one ship, the Desna, commanded by the Midshipman Juliano Lombard. Suvorov's military skill and the bravery of the Russians led to a Turkish defeat on 1 October 1787.

Two days later Commander Alexander Veryovkin fought the entire Turkish fleet at Ochakov for two hours with his floating battery. Recovering from the daring attack, the Turks made an attempt to seize Veryovkin's ship, and nature once again favoured the Turks. Heavy waves sank Veryovkin's ship, and he and his crew were taken prisoner. With the arrival of an unusually severe winter, action in the Liman Firth ceased. The following year the rowing squadron came under the command of Prince Karl Nassau-Ziegen and the supporting army remained under Suvorov. Prince Potemkin dismissed Mordvinov, and the sailing squadron in the firth was commissioned to the hero of the Archipelago Expedition, Brigadier Panaiothos Alexiano and to RearAdmiral Jones. John Paul Jones, a Scot by birth, was the most celebrated naval hero of the American Revolutionary War. At the conclusion of the war between the United States and England Jones had moved to Paris, where he received an invitation from Catherine II to become a rear admiral in the Russian fleet. Unfortunately, Jones and Nassau-Ziegen were envious of each other's successes, a situation which adversely affected the merits of these naval leaders in subsequent battles.

Kapudan Pasha Hassan brought 98 pennants to Ochakov. On 18 May the formidable Turkish squadron entered the firth. The Turks intended to destroy the Russian vessels, seize the fortress of Kinburn and repulse Potemkin's attack on Ochakov. Captain Second-rank Reingold Saken was the first to meet the Turks, and his large boat was quickly surrounded by enemy galleys. The Turks had already begun to celebrate victory when suddenly an explosion rocked the waters. Captain Saken's ship had exploded, killing him and inflicting heavy damage on the enemy.

On 7 June the Russians stymied an attack on Ochakov. In response Hassan Pasha sent six more ships of the line into the shallow firth. The decisive battle for Ochakov took place on 17-18 June 1788. Fifty-eight Russian vessels with 400 guns and 5,500 men attacked the Turks, who had twice that force both in men and guns. In Jones's squadron there were only one big frigate and one large warship, the 66-gun Vladimir. Hassan Pasha immediately deployed ten ships of the line.

The battle continued all day. Through skilful maneuvering, Russians managed to set fire to the Turkish flagship. The Turks were forced to retreat, abandoning their burning flagship to the mercy of fate. Recalling the lessons of Chesma, Hassan Pasha tried to lead his ships out of the firth under cover of darkness. However, Suvorov had prepared for such a possible outcome, and a Russian battery, camouflaged on the Kinburn spit, awaited the enemy. The waters of the firth were lit up by the flashes of shots as the Russian rowing flotilla attacked. The Turks lost five frigates and three ships of the line, one of them seized by the Russian fleet as a prize of the battle. Two thousand seamen of the Ottoman Empire perished and 1,673 were taken prisoner. The Russian fleet lost 85 seamen and its floating battery.

Supported in his role as first flag-officer of the flotilla by Field-Marshal Potemkin, Prince Nassau-Ziegen attributed the success of the naval campaign against the Turks to himself and belittled the valour and energy displayed by Admiral Jones and Brigadier Alexiano. The news of the battle that reached St. Petersburg was coloured by Nassau-Ziegen's personal jealousies.