De Monts was determined to try the climate of Port Royal, and to endeavour to establish a settlement there.  Two barques were fitted out and laden with the frame work of the buildings at Ste. Croix.  Champlain and Pont-Grave had set out before to select a favourable site around the bay, well sheltered from the north-west wind.  They chose a place opposite an island at the mouth of the river de l’Equille, as being the most suitable.  Every one was soon busily engaged in clearing the ground and in erecting houses.  The plan of the settlement, says Champlain, was ten fathoms long and eight fathoms wide, making the distance around thirty-six fathoms.  On the eastern side was a storehouse occupying the width of it, with a very fine cellar, from five to six feet deep.  On the northern side were the quarters of Sieur de Monts, comfortably finished.  In the backyard were the dwellings of the workmen.  At the corner of the western side was a platform, upon which four cannon were placed, and at the eastern corner a palisade was constructed in the shape of a platform.  There was nothing pretentious or elegant about these buildings, but they were solid and useful.

The installation of the new settlement being now complete, de Monts returned to France, leaving Pont-Grave in command.  During the absence of de Monts, Champlain determined to pursue his discoveries along the American coast, and in this design he was favoured by de Monts, as the latter had not altogether abandoned his idea of settling in Florida.  The season, however, was too far advanced, and Champlain therefore stopped at the river St. John to meet Schoudon, with whom he agreed to set out in search of the famous copper mine.  They were accompanied by a miner named Jacques, and a Slavonian very skilful in discovering minerals.  He found some pieces of copper and what appeared to be a mine, but it was too difficult to work.  Champlain accordingly returned to Port Royal, where several of the men were suffering from scurvy.  Out of forty-five, twelve died during the winter.  The surgeon from Honfleur, named Deschamps, performed an autopsy on some of the bodies, and found them affected in the same manner as those who had died at Ste. Croix.  Snow did not fall until December 20th, and the winter was not so severe as the previous one.

On March 16th, 1606, Champlain resumed his explorations, and travelled eighteen leagues on that day.  He anchored at an island to the south of Manan.  During the night his barque ran ashore and sustained injuries which it required four days to repair.  Champlain then proceeded to Port aux Coquilles, seven or eight leagues distant, where he remained until the twenty-ninth.  Pont-Grave, however, desired him to return to Port Royal, being anxious to obtain news of his companions whom he had left sick.  Owing to indisposition, Champlain was obliged to delay his departure until April 8th.