Born in a family of the lesser nobility, he graduated from the Saint Petersburg Naval Academy and later found employment there. During the Seven Years' War Nagayev headed the hydrographic expedition to the Prussian shores. He also compiled the first atlases of the Bering Sea and Baltic Sea, which were published in 1752. Despite the absence of a meridian grid, Nagayev's maps were used for a further fifty years. In 1764-65 Nagayev became the supreme commander of the Kronstadt port. He was promoted to the rank of admiral in 1769.