Several operators run boat trips from Boothbay Harbor's pier, the most popular being whale watching cruises out to Jeffreys Ledge and other feeding grounds off the coast. Finback, minke, and humpback whales are regularly sighted from late June through September. Balmy Days Cruises and Cap'n Fish's Whale Watch are among the established operators.
Puffin-watching trips to Eastern Egg Rock, about an hour offshore, are a draw in their own right — the island is a successful restoration site where Atlantic puffins were reintroduced in the 1980s after being driven locally extinct. The boat trips coincide with the breeding season (June–August) when the birds are ashore and easy to observe. Lighthouse tours, lobster-boat excursions, and sailing day trips are also available from the harbour. Book in advance during peak summer season.