Beginning in the 1980s, sewage flowing through the gulch entered into the Tijuana River, contributing to water contamination; since then mitigation efforts have been undertaken, but are defeated by rainfall.

[11]: Sedimentation And Erosion Study: 6  When the base flow is absent, sewage from Mexico would follow the path of the creek were it not diverted for treatment.

[19][26] The canyon began to be referred to as Smuggler's Gulch as far back as the 1880s due to smuggling of livestock from Mexico into the United States.

[27] In 1889, a schoolhouse was built near the mouth of the gulch and continued to operate until 1941; prior to its closing, it had been the southwest most school in the United States.

[4]: 63 [15]: 16  By the 1970s, significant croplands which had existed with the Tijuana River Valley began to be abandoned, with the exception of those near the mouths of the gulch and nearby Goat Canyon.

[32] In May 1992, Pat Buchanan visited Smuggler's Gulch as part of his presidential campaign and delivered a news conference where he spoke out against illegal immigration and in favor of increased border security.

In addition to news reporters and Buchanan supporters, the event was also witnessed by a number of migrants and neo-Nazis led by Tom Metzger.

[13] Beginning in the latter half of the 1980s, work began to collect sewage flows within the gulch but was insufficient to capture all of it, with over 100,000 US gallons (380 kL) continuing into the estuary every day in 1987.

[25] In the 1990s, the City of San Diego purchased land at the mouth of the gulch and utilized it as a toxic waste dump, importing contaminated soils from Sorrento Valley.

[25] By the mid-1990s, millions of gallons of sewage were flowing through the gulch, leading to additional attempts to mitigate the issue by construction of additional pumps and pipes to the then-newly constructed International Boundary Wastewater Treatment Plant;[25] however, when it rains these pumps are insufficient to collect the polluted waters from Tijuana, which then flow into the Tijuana River and thence into the Pacific Ocean.

[41] In 2002, a Border Patrol agent died when her vehicle toppled down the gulch's steep slopes;[27] this was one of four deaths that were attributed to narrow switchback roads which existed on the canyon walls.

[45] Beginning in 2005, environmental laws were waived, as authorized by the Real ID Act, in order for the Mexico–United States barrier to be built in the gulch and in nearby Goat Canyon.

[53] Beginning in October 2011, native vegetation began to be installed by United States Customs and Border Protection (CBP) in order to rehabilitate areas affected by the installation of the border barrier across the gulch;[54]: 29  this has stabilized the fill, which has seen reduction of height change from 0.5 centimetres (3⁄16 in) per year, to 0.1 centimetres (1⁄32 in) per year, all but eliminating sedimentation.

[58] Due to the decrease in people crossing the border in the gulch, sensitive areas in the Tijuana River Estuary are no longer trampled upon.

[62] As of October 2015[update], the gulch south of Monument Road and north of the Mexico–United States barrier is owned by the County of San Diego.

Since that time, an assortment of surface and subsurface discoveries has been attributed to CA-SDI-10669, resulting in the documentation of an extensive shell and lithic scatter by Seth Rosenberg in 2008.Unfortunately, the predominance of mottled deposits including modern trash intermixed with elements of the prehistoric occupation of the area indicated that this portion of Site CA-SDI-10669 did not retain integrity.