It runs from its source in the Laguna Mountains southwestward where it is impounded by two dams, Barrett and Morena, to supply water to the city of San Diego.

The Arroyo de las Palmas, the main tributary of the Tijuana River, flows out of the mountains to the east into the reservoir behind the Abelardo L. Rodríguez Dam.

Its lower reaches provide the last undeveloped coast wetlands in San Diego County amidst a highly urbanized environment at the southern city limits of Imperial Beach.

The Tijuana River rises in the Sierra de Juárez of northern Baja California, approximately 45 mi (70 km) ENE of Ensenada.

The Tijuana River enters the Pacific 10 mi (15 km) south of downtown San Diego at the southern city limits of Imperial Beach.

[6] Flooding in the Tijuana River had been a concern for both the United States and Mexico because it would lead to sewage runoff and would ultimately cause property damage to the surrounding area.

[10] Flooding due to high rainfall and sewage blockage continues to be a concern that endangers surrounding areas because of the wastewater pollution found in the river.

The Tijuana Slough Refuge protects one of southern California's largest remaining salt marshes without a road or railroad trestle running through it.

[17][6] As such, the issue of sewage in the Tijuana River predates other news stories about the Mexico–United States border within the San Diego–Tijuana region by several decades.

[22] In the 1960s an emergency link from Tijuana into the San Diego Water System was created, by the mid-1980s it was taking in about 15 million gallons a day of sewage.

[24] In 1980, Brian Bilbray, as Mayor of Imperial Beach, dammed the river with a skip loader to block the flow of sewage crossing the border.

[26] In April 1990, the U.S. Environmental Protection Agency found lead and mercury in the waters of the Tijuana River watershed that exceeded multiple times U.S. standards, prompting fears of outbreaks of malaria and encephalitis.

However, when it rains, the amount of sewage can increase to 27 million gallons per day, and the pump which funnels water to the treatment plant is shut off so it isn't overcome.

[36] Yet, in 2017, it was found by Proyecto Fronterizo de Educacion Ambiental that the release from the plant exceeded Mexico's minimum federal standards on bacterial levels.

[42] The impact of the spill affected waters as far north as Coronado, and was described by Imperial Beach Mayor Serge Dedina as "a tsunami of sewage",[39][43] and "deliberate".

[45] Repairs of the sewer pipe were completed in late February 2017, but the exact dates when the sewage began and stopped entering the river were unknown as of March 2017, leading to calls for an investigation.

[47] In mid 2017, Border Patrol agents reported sewage flowing into the Tijuana River from Smuggler's Gulch, and Goat and Yogurt Canyons.

[50] In March 2018, Customs and Border Protection began to search for solutions to the sewage issue, after more than six dozen Border Patrol agents were negatively impacted by their contact with sewage in the Tijuana River Valley;[51] this included taking water and soil samples to assess the contamination levels which exist in waters and areas around the Tijuana River watershed.

[57] In February 2019, testing revealed significant pollutants flowing northward from Tijuana including DDT, hexavalent chromium, pathogens, and carcinogens.

[59] In mid 2019, it was proposed that all water flowing northward on the Tijuana River be diverted and processed at the San Diego-Tijuana Wastewater Treatment Plant.

[61] In early September 2019, an additional 116,000,000 US gallons (440,000 kL) of contaminated water flowed into the Tijuana River, leading to continued beach closures.

The most recent data showed that over 34,000 people in 2017 got sickened by the pollution and sewage in Imperial Beach according to a study that a University of California San Diego professor did.

[65] For years, public health officials say they have sampled beach waters of south San Diego County for fecal microbes, getting counts as an indicator for pathogens such as enterococcus, E. Coli, salmonella and MRSA.

[64] From 2018 to 2024, more than 100,000,000,000 US gallons (380,000,000 kL) of wastewater have flowed from Mexico into the United States via the Tijuana River according to the International Boundary and Water Commission.

[66] In March 2018, due to sewage in the Tijuana River, Chula Vista, Imperial Beach, and the Port of San Diego sued the International Boundary Water Commission.

[73] Over 30 federal, local, state, private and other interested groups want to develop binational long-term goals to address wastewater treatment and debris-related improvements.

Due to the fences, the amount of illegal entry into the United States along the border south of the Tijuana River has been significantly reduced.

[101] Sewage from the river impacts water quality, which can lead to surfers becoming ill;[102] one source describes that area as "virtually unsurfable due to pollution.