It is situated within the 112-acre (0.45 km2) Salmon River Falls Unique Area, managed by the New York State Department of Environmental Conservation.

The falls and surrounding land was owned by the Niagara Mohawk power company prior to 1993, when ownership was transferred to New York State.

Historically, the falls were the natural upstream limit for spawning salmon in the river prior to the construction of the Lighthouse Hill Dam.

The 164-acre (0.66 km2) reservoir was created with the completion of the Lighthouse Hill Dam in 1930, which currently represents the first barrier to upstream migration for salmon and trout.

[6][7] The Salmon River passes through a region with sedimentary bedrock composed of limestone, shale, siltstone and sandstone.

After the uplifting of the Appalachian Plateau approximately 220 million years ago, numerous streams in the area, including the Salmon River and its tributaries, began to cut gorges (locally known as "gulfs") through the bedrock.

The geologically recent Pleistocene glaciations further influenced the landscape approximately 12,000 years ago; the region's soils in particular are the result of deposits of glacial till from this time.

[4]: 24 Prior to European colonization, the Salmon River and its surrounding area was important to the Iroquois Confederacy as seasonal hunting and fishing grounds.

[16][17] The river also served as passage to interior hunting grounds, and was described in 1688 as "the place where the greater part of the Iroqouis embarked to go upon the trail of the beaver", in reference to their excursions into the Lesser Wilderness, now known as the Tug Hill.

[19] La Famine was described as a "well-known stopping-place upon the eastern shore of Lake Ontario for the weary hunter and the bold explorer, and the spot where even armies encamped, and the ambassadors of hostile nations met in solemn council.

"[18] Records from Jesuit missionaries as early as 1657 make note of Iroquois fishermen taking large quantities of Atlantic salmon from the river, which would then be dried or smoked to preserve it for the upcoming winter.

[15] One early source observed that the river contained so many salmon that the Iroquois "often brought up a hundred at one cast of the net.

Their control was short-lived, however, as the United States gained its independence from Great Britain following the American Revolution in 1783; the region's Iroquois were also substantially weakened, having suffered losses due to siding with the British during this time.

[15] The Salmon River underwent extensive changes in the early 1900s with the construction of hydroelectric dams and their associated reservoirs.

[21] On September 30, 2010, large amounts of rain fell within a matter of several hours in the Salmon River drainage area, ranging from 2.66 to 6.51 inches (6.8 to 16.5 cm), causing historic flooding.

This same period of time saw the stocking of 144,000 Atlantic salmon fry, however poor survival of these fish led to this program being discontinued as well.

Poor river conditions, pollution, and the impacts of parasitic sea lampreys contributed to the failure of these stocking programs.

Alewife populations exploded, sometimes to the point of causing die-offs large enough to require the use of bulldozers along Great Lakes' beaches.

[25] Seeking to control prey fish populations, the aggressive stocking of coho and Chinook salmon resumed throughout the Great Lakes and their tributaries.

Between 1976 and 1977, possession of salmon caught in Lake Ontario or its tributaries was banned due to elevated levels of chemical contaminants such as Mirex and PCBs.

[28] For many years, flow rates in the river's main stem below the Lighthouse Hill Dam changed frequently and dramatically as water was released in response to variable demands for electricity.

Paid-only access is available on the stretch of the river below Pulaski and above the NYS Route 3 bridge in an area where no easements exist, known as the Douglaston Salmon Run.

[39] Bait presentation strategies must therefore stimulate the aggressive nature of these fish to provoke them to strike, as they do not feed after entering the river.

[43] Snagging, the indiscriminate taking of fish using weighted hooks that are ripped through the water with quick jerking motions, was controversially outlawed on the Salmon River in the early 1990s.

[28] It had previously been argued that snagging was ethical due to the difficulty in enticing Chinook and coho salmon to strike, as these fish die after spawning and do not feed once they enter the river.

[28] The popularity of salmon fishing in the general Lake Ontario region did wane in the late 1990s, and the snagging ban may have contributed to this decrease.

[3] In addition, the level of sportsmanship and the general atmosphere along the Salmon River is described as having improved since the ban was put in place.

Enforcement of the ban is a major priority for Environmental Conservation Officers who patrol the river during peak salmon season, sometimes using stealth and undercover techniques to catch snaggers in the act.