Thousands of people streamed back to this historic southern city Monday where new levees hastily built from clay and stone held back floodwaters that have inundated much of Pakistan.

Thousands who fled the waters that inundated neighboring towns complained about the shortage of food and water as they camped in a vast Muslim graveyard on a hill near Thatta city.

Thatta, which is about 75 miles (125 kilometers) southeast of the major coastal city of Karachi, contains several well-known mosques, including one built by Shah Jahan, the ruler of the Mughal Empire in India in the 1600s....