The fleet was modest by European standards: the patache Santa Maria da Candelária, the caravelão Santa Maria das Graças, and the large speedboat Assunção. Aboard were 150 men, led by Captain Francisco Caldeira Castelo Branco, who took the grandiose title of Discoverer and First Conqueror of the Amazon. They dropped anchor at what the native Tupinambá called Mairi, on the eastern shore of the bay. The engineer-major Francisco Frias de Mesquita went ashore and began laying out the Forte do Presépio, a wooden fortification that would give the new settlement a defensible position. Castelo Branco called the place Feliz Lusitânia. The problem, from a Spanish legal perspective, was that under the 1494 Treaty of Tordesillas, the entire Amazon basin belonged to Spain. The solution was the Iberian Union, the temporary dynastic merger that had joined the two crowns in 1580, making the distinction functionally irrelevant.

The fort had to earn its keep almost immediately. In the decades after 1616, Guajará Bay was contested water. Dutch, English, and French ships pushed into the estuary looking to establish trading posts and alliances with indigenous groups, seeking access to the spices, hardwoods, and medicinal plants known collectively as the drogas do sertão. None of them succeeded in settling permanently on the bay. The Portuguese pushed them steadily northward until they found themselves in the Guianas, where their descendants remain: French Guiana, Suriname, and Guyana exist in part because the Portuguese kept the Amazon mouth and nobody else could break through. The bay was the gate, and the gate held.

Guajará Bay is tidal freshwater, not salt. Mangroves line the quieter shallows. Igapó, the seasonally flooded forest that is one of the signature ecosystems of the Amazon, fringes the river mouths. Floodplain várzea spreads behind the levees. The surrounding upland is tropical rainforest, the Atlantic Forest giving way to the Amazon biome. The insular portion of Belém municipality, a scatter of 42 islands totaling 329.9 square kilometers, lies offshore in the bay; these are the islands that supply açaí to the city's famous waterfront market every morning. The largest and most visited is Mosqueiro Island, an 11,000-hectare land mass to the north of Belém whose 17 kilometers of beaches draw weekend crowds escaping the capital's equatorial heat.

There is a specific story behind Mosqueiro's name that has nothing to do with mosquitos. The Tupinambá who lived on the island had developed a technique for preserving fish called moqueio, in which fish were smoked on wooden racks over low fires. A moqueio was the structure where this smoking happened. Early Portuguese writers adopted the word, spelled it Mosqueiro, and applied it to the island where the practice was widely observed. The name has survived for four hundred years. The fish smoking has mostly not. Today Mosqueiro is a resort district, connected to Belém by the Governador Almir Gabriel Bridge, but the etymology holds: the word on the maps is a Tupi-Guarani word from a vanished culinary technique.

The bay that was once a highway of empire is now a working harbor and a compromised ecosystem. Water pollution from disorderly coastal occupation and inadequate sanitation, mangrove loss, and sedimentation are the familiar problems of a bay adjacent to a metropolitan area of more than a million people. The city's growth has pushed up against and sometimes into the water, informally and unplanned. Pará state authorities and environmental organizations run conservation and awareness programs, creating protected zones and undertaking reforestation, though the pressures persist. The fair at Ver-o-Peso, the sheds along the Avenida Boulevard Castilhos França, the cruise ships that occasionally call at the port, all depend on the water. The water has a long memory. It knows what passed this way before.