After Jolliet and Marquette completed their expedition, they parted in Green Bay. Jolliet and his companions were caught in the treacherous Lachine rapids near Montreal. His men were drowned, and his charts, maps, diagrams and journal were lost. He escaped by clinging to a rock. He reported to the governor and reproduced his documents from memory.
In 1675, Jolliet married Claire-Francoise Bissot, a French Canadian. Four years later, he traveled the Saguenay and Rupert Rivers to Hudson Bay to gain intelligence about British activity in the region. When the governor awarded him Anticosti Island for his service, Jolliet, his wife, their four children and six servants moved to the island and erected a fort in 1680. In the winter of 1690, Sir William Phips and his troops occupied the island fort after a failed attack on Quebec.
Jolliet was appointed Royal Hydrographer in 1693, and studied hydrography in France. In 1694, he went on a 5½ month expedition along the coast of Labrador from the Strait of Belle Island to Zoar. He recorded the details of the area and noted the customs of the Inuit peoples. His journal is the earliest known survey of that area. On April 30, 1697, he was granted property southwest of Quebec which he named Jolliest. That year he became a professor of hydrology at the University of Quebec.
In May, 1700, Jolliet left for Anticosti Island, but he never arrived, and his body was never found. A Funeral Mass was said for him on September 15, 1700. His descendants living in east Canada and the US are his greatest legacy. He is honored through the numerous geographical places and the Louis Jolliet Rose named for him by Agriculture and Agri-food of Canada.
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