Complex sentence: Timber pirates continued to thrive in the Great Lakes for several years afterward and at the same time there were pirates on the northern Mississippi River and the American navy launched another separate operation against timber pirates in the Calcasieu River of Louisiana.
Split into simpler sentences: Timber pirates continued to thrive in the Great Lakes for several years afterward though and at the same time there were pirates on the northern Mississippi River. The American navy also launched another separate operation against timber pirates in the Calcasieu River of Louisiana.