Until the latter half of the nineteenth century, the East Harbor was a natural embayment deep enough to shelter Provincetown's fishing fleet during the winter, and was connected to Cape Cod Bay through a 1,000-foot-wide (300 m) inlet.

[1] Until late in the 19th century, there were no roads leading in or out of Provincetown – the only way to travel by land to the rest of Cape Cod was to first walk north, traversing a series of tall, rolling sand dunes, and to then follow the thin strip of beach along the northern shore line, known as the "backshore".

[1][5] The harbor was artificially separated from Cape Cod Bay and cut off from tidal flow in 1868, when a dike was constructed across the inlet to facilitate the laying of track for the arrival of the railroad.

This ~700-foot-long (210 m), 4 feet (1.2 m) diameter culvert had been fitted with clapper valves to allow freshwater to drain out of Pilgrim Lake, but prevented marine tides from flowing back into the system.

Despite limits on tidal exchange imposed by the pipe's small diameter, and the distance that it travels underground, they have observed a substantial response in the recovery of salinity and estuarine biota.