During the 1654–1667 war with Russia and during the Great Northern War (1700–1721) Merkinė suffered greatly from Russian and Swedish armies and lost its strategic and economic significance. Merkinė was burned again by the Russian army during the 1794 Uprising which tried to liberate the Polish–Lithuanian Commonwealth from Russian influence. In 1794 town inventory river port by Nemunas river is mentioned, also Nemunas and Merkys rivers were evaluated as suitable for navigating. In 19th century documents Merkinė was mentioned as river trade center in which river trade ships were built.