Their leader, a tyrannical type in the likes of Saddam Hussein, ordered a large number of boats to be constructed. He had each household in the city that was closest to the sea construct one boat. The thing you must understand is that since the surface of a 2d planet is linear, to pass anything while traveling, you have to go either over it or under it. To store in one place the number of boats that was needed would have required an extremely deep hole. Deep holes are problematic in 2d because of numerous reasons.
Air pockets can form extremely easily, easily suffocating anyone trapped inside.
Limitations in 2d make extracting dirt from the deep quite difficult. The best way to store things is to spread them out across the surface. The residents of the city slaved away for weeks, constructing the boats in the least time possible. Numerous skipped meals and lost hours of sleep later, the army's water transportation had been completed. The leader ordered the advance to begin.