Why were the pilgrims so miserable once they got to the New World?

First, the Pilgrims had already endured a rough Atlantic voyage. Ships back then did not carry much in the way of fresh fruit and vegetables, so the Pilgrims were already in dire need of vitamins. Also, sanitation was an afterthought on these ships. Fresh water was at a premium, so bathing was out of the question. There was also the issue of crowding. The Pilgrims arrived in the New World already distressed and short of food, and they had to face the New England winter under these conditions.
Many died on board the ship while they waited for housing to be built in the new colony. There was also fear—no one knew about the nature of the Native Americans who lived in the area. The initial goal of the Pilgrims was to arrive further south and closer to the Jamestown area, so they were definitely in uncharted territory. While the Pilgrims were thankful to have a new place to practice their religion, there was still much anxiety as to how to fill basic needs.