The river runs through a valley that may have been a larger riverbed before the last Ice Age, and it divides Queens into western and eastern halves.

[7][8] Prior to the lakes' construction, the creek meandered through tidal marshes in the larger valley within the present-day park;[9][10] its mouth was at Flushing Bay, a 6,200-acre (2,500 ha) water body on the East River.

[12] Afterward, the Flushing River re-emerges from the ground, where it partially divides a 19-acre (7.7 ha) plot of land occupied by the park's pitch and putt golf course.

[13] It then flows underneath the Tide Gate Bridge, where the fresh water river mixes with the saltwater from Flushing Bay.

[24] The southern branch, which has been infilled,[25] originated at Town Pond at the modern-day intersection of Northern Boulevard and Main Street, which was filled in 1843;[26] the creek then flowed north.

[24] The northern branch, which still exists in truncated form, originated at the site of the George U. Harvey Playground,[23] near the intersection of 20th Avenue and the Whitestone Expressway in Whitestone,[27] and flowed south through the present sites of College Point Fields, Flushing Airport, and College Point Corporate Park.

[28][29] Several underground pipes, as well as man-made drainage ditches on the New York City Police Academy campus and north of 28th Avenue, carry the creek from the airport to the Flushing River.

[34] The present-day Long Island Expressway crosses the river to the north, slightly east of the site of Strong's Causeway.

[40] The causeway was replaced in 1937 by a bridge carrying the then-newly built Horace Harding Boulevard,[41] and was rebuilt into the present Long Island Expressway in the late 1950s.

[45][46] The LIRR trestle, located directly to the north of Tide Gate Bridge, contains a small opening for water to pass through.

With the 1939 New York World's Fair, the creek was dammed to the south, and the Roosevelt Avenue bridge ceased to be a usable drawbridge.

[52] The LIRR's former Whitestone Branch was carried by a single-tracked wooden trestle north of the Roosevelt Avenue bridge, which contained a small drawbridge span.

[14] The land around Meadow Lake contains open grass, picnic and grilling areas, and baseball and cricket fields as part of Flushing Meadows–Corona Park.

[74] The American Small Craft Association also houses a fleet of over a dozen 14.5-foot (4.4 m) sloop-rigged sailboats, used for teaching, racing, and recreation by the club's members.

[71] The area around Willow Lake originally also contained sports fields and park trails,[1][83][67] until it was fenced off and turned into a preserve in 1976.

[85][86] During at least three glacial periods, including the Wisconsin glaciation around 20,000 years ago, ice sheets advanced south across North America carving moraines, valleys, and hills.

During glaciation, the meadows surrounding the Flushing River were formed just north of the terminal moraine that runs across Long Island, which consisted of sand, gravel, clay and boulders.

[97] The earliest fixed crossing of the Flushing Creek was the Northern Boulevard bridge, built in 1801 and rebuilt six times through 1980.

[106] Degnon envisioned using the site to create a large industrial port around Flushing Bay, similar to a terminal he developed in Long Island City.

The plan envisioned widening Flushing River and creating docks for ships, with numerous factories and freight facilities.

[110] The next year, surveys were made for the construction of a 5.4-mile (8.7 km) canal to connect Flushing River and Newtown Creek, plans for which dated back at least a century.

[111] To create the port, Degnon proceeded to fill the Flushing River wetlands using household coal refuse ashes and street sweepings from Brooklyn.

[107][112] The filling for the north meadow was complete in 1916,[107] but the prospect of creating a port was halted in 1917 by material restrictions caused by World War I, and a lack of federal support for the project.

Over the years, pollution from the Willets Point industrial area, surrounding highways, and dumping made the river a health hazard.

[127] Furthermore, under the intervention and proposal of both Morton Povman and Peter Vallone, a group of high city officials agreed to begin immediate work on the long-term task of cleaning up this waterway.

The late Abe Wolfson, founder of the Queens Historical Society, became active in the fight to restore the river to its original condition.

[132] Plans to combine Meadow and Willow Lakes were proposed in 2005 as part of the failed New York City bid for the 2012 Summer Olympics.

Following the failure of the bid, the New York City Department of Environmental Protection sought a scaled-back restoration plan for the lakes.

[137][138] In addition, the redevelopment of the industrial Willets Point neighborhood on the left bank of the river was announced in 2007,[139] and after several delays, was restarted in 2018.

[140] Following news of these redevelopments, an organization called the Friends of Flushing Creek was created in mid-2014 to advocate for a greater cleanup of the river and bay.