Algodoal has various options for guided and do-it-yourself excursions. You can canoe (R$2) up the canal at Praia do Farol to spot birds and sometimes monkeys (best at sunset); visit Lago de Princesa (best April to June), walk or boat to the village of Fortalezinha, or even walk around the island.
Sunset is the best time to spot birds and wildlife, including the timid but radiant guará (scarlet ibis). However, high tide is when the canals are deepest and canoes can penetrate the furthest. Ideally, you'll be visiting when sunset and high tide happen to coincide! At high tide, you can canoe clear to Praia do Mupéua on the other side of the island (and from there walk back to town, about 7km) or else return along another canal to Porto do Mamede, Algodoal's main dock.
Partway up the canal from Praia do Farol, a path cuts through the forest and low sand dunes to Lago da Princesa and onward to Praia da Princesa (2km to 3km total). Boatmen can drop you at the path, and you can visit the lake, then return by foot along the beach (4km). The lake is just a small lagoon, and worth visiting only when full (April to June).
Another option is visiting Fortalezinha, a small village on the other side of the island, where you can walk the beach and grab lunch at one of several small restaurants. The boat ride from Algodoal to Fortalezinha is scenic but pricey (R$100); alternatively, you can catch a canoe (R$3 per person) from Porto do Mamede to the nearby community of Camboinha and follow well-marked paths from there.
From Fortalezinha it's possible to walk counter-clockwise back to Algodoal. (The reverse is much less pleasant, as you'll be walking against the wind.) It's a long (14km) but scenic walk. However, there's a powerful furo (tidal inlet) about halfway around that should never be crossed on foot. Wait for a fisherman to ferry you across or else turn back.
On any trip, be sure to bring mosquito repellent, water and sun protection.
Guided trips range from R$50 to R$180 per person, depending on what you do. For simple trips, boatmen can be hired at the mouth of the canal at Praia do Farol. Many hotels can recommend guides; Pousada Marhesias has the most in-depth information, including simple maps of the island.