The Swallows intend to sail in the Goblin to Hamford Water and camp with their father, but he is called away on naval business. Instead he maroons them with a small dinghy on an island. Before he leaves, Father gives them an outline map of the area they decide to call Secret Water and suggests they survey and chart the area before he returns to pick them up. For a surprise, he has arranged for the Amazons to come down from the Lake District and join them with another dinghy.
They see some mysterious footprints which turn out to belong to the Mastodon, a local boy. He mistakes them for the Eels, another family who camp in the area regularly. Later the Eels arrive and are initially hostile before they settle down for a friendly war.
It seems that due to the distractions of war and being cut off by the tides, the chart will not be completed. However early in the last morning two separate groups of children complete it.