Sunswick Creek ran through Queens until the late 19th century, originating in the south of the Ravenswood area. These maps below are from 1873.
The waterway was above ground at least through the 1870s. Eventually, however, it was completely covered over, though it's apparent inside the thing that different parts of the tunnel were covered over at different times.
Flushing River still exists, though it is a far different
watercourse than it was originally. When the town of Flushing was
settled in 1645 along the marshy streams in what is now Flushing
Meadows/Corona Park, the creek ran from Kew Gardens (where the old site
of the headwaters of the creek is marked by the street Vleigh Place,
after the Dutch for Valley).
The marshy land watered by the creek
in Flushing Meadows, which today is a green and landscaped expanse—was
famously turned into a giant ash dump in the 19th century, run by the
Brooklyn Ash Removal company under “Fishhooks” McCarthy.
In the novel The Great Gatsby, Fitzgerald describes how the area looked in the 1920s:
is a valley of ashes—a fantastic farm where ashes grow like wheat into
ridges and hills and grotesque gardens, where ashes take the forms of
houses and chimneys and rising smoke and finally, with a transcendent
effort, of men who move dimly and already crumbling through the powdery
air…. The valley of ashes is bounded on one side by a small foul
river, and, when the drawbridge is up to let barges through, the
passengers on waiting trains can stare at the dismal scene for as long
as half an hour.”
Other than the ashes, swamps occupied
the land, fed by the marshy drainage ditch of Flushing River. But in
just three years, between 1936 and 1939, the city covered the vast
fields of ashes, dug out a new channel for the river, filled in the
swamps, created the new Meadow Lake, and landscaped 1,200 acres to
create the utopian World’s Fair of 1939.
Robert Moses, who was a
driving force behind the transformation, wrote that his teams “leveled
the ash mountains, and rats big enough to wear saddles, with white
whiskers a foot long, gazed wistfully at the bulldozers and junkies who
disturbed their ancient solitary reign.” By 1939 it was impossible to
see any evidence of either the ash landfill, or of the natural
topography that had replaced it.
For more information, see http://en.wikipedia.org/wiki/Flushing_River.
The article mentions that Flushing Creek received water from Fly Creek,
Ireland Creek, and Horse Brook; please email me if you know anything
more about any of these other watercourses.
From Long Island City by Thomas Jackson & Richard Melnick:
Cove was the site of a Native American settlement. Fresh water came
from a small stream, later called Linden Brook, that flowed along
Astoria Park South. Here, they cleared woodlands to grow corn,
harvested oysters and clams, and caught fish.
Linden Brook is hard to find on maps. Apparently it was a small
stream, and by the time the area was settled enough for good maps to be
produced, it had mostly disappeared underneath urbanization. However,
the 1873 Beers maps of Long Island City and region show it, though just
barely. Below is a large section of the map. Pot Cove is the area
directly below Hell Gate and Ward's Island, above the spur of land that
juts out above Hallet's Cove.
Below is a closer crop of the Pot Cove area. The Linden Brook is visible as a wavy line in the upper right, below Linden Street.
And below is a very close crop of the area; Linden Brook is the wavy
line on the right, and outlets into the water on the left. Linden
Street, obviously, is named after the brook; today this is the line of
Hoyt Avenue and Astoria Park South.