California's border with Baja California is a complex region with unique environmental issues. Our Borderlands series takes a deeper look at this region unified by shared landscapes and friendship, and divided by international politics.

It's been weeks since the last substantial rain, but standing puddles and muddy spots still remain on trails on both sides of the international border along the San Diego and Tijuana coastline. Entire sections of trails and roads that meander from the Tijuana River Valley's marshlands in San Diego to Friendship Park at the international border wall get washed out or flooded after every downpour.

The coastal border region is particularly vulnerable to rains. Storms send muck and sewage down canyons, into channels, and finally gets discharged into the Tijuana River and the Pacific Ocean, prompting pollution warnings and beach closures in both countries. Contamination and cross-border pollution has been a fraught topic for years, but never more so than now, ahead of a rainy season in which a historically powerful El Niño appears imminent.

Historically, water pollution and marine pollution here have been blamed on Mexico. It's easy to do because Tijuana is on higher ground than the San Diego side, and polluted runoff flows downhill. But like so many border issues, the pollution's actual origin and eventual destination have deeper causes in the history, politics, and socioeconomics of both countries.

Sarah Giddings, a researcher with the Scripps Institution of Oceanography, is a project leader for CSIDE, the Cross Surfzone/Inner-shelf Dye Exchange, which is using bright pink fluorescent dye to track wave dynamics and water movement from the estuary's mouth up the California coast. The team hopes that the experiment, which wrapped up last week, will provide more insight into the path contaminants take as they travel up the coast by providing better ways to model wave and surf dynamics.

"We were surprised that the dye was still pretty strong by the time it makes it really far north," said Giddings. "It happens very quickly, and it's not as diluted as we may have predicted." That means that the ocean doesn't disperse the pollution as quickly as had been thought, raising the possibility of more widespread damage to marine and coastal life.

Wave dynamics aren't the only complicated part of the Tijuana River pollution puzzle, thanks to initiatives like the North American Free Trade Agreement (NAFTA) -- which allows internationally owned companies to set up shop in Mexico -- California's relationship with the Mexican state of Baja California Norte, and the political situations in both the United States and Mexico.

"It's all part of the same system," said Magdalena Cerda, an environmental activist and director for the Environmental Health Coalition's Border Justice campaign. "It's all connected. The maquiladoras, the factories, work on two principles: lower salaries and fewer environmental regulations. There's no multinational obligation to pay fines in Mexico."

Each year, factories in Baja California are supposed to pay fines if they pollute, but many - especially the smaller ones - simply don't. Others bury or dump their waste, which then is eventually washed into the Tijuana watershed. Another multinational agreement allows used tires to be imported from the United States into Mexico, which are used on cars and as building materials in colonias and shantytowns, and which are inevitably part of the debris that finds its way back north, to California beaches.

"I think we're getting better at cooperating across the border," said Aimee Barnes, Deputy Secretary for Border and Intergovernmental Relations with the California Environmental Protection Agency. "We've got an active border program that's been here in the agency for a number of years, and we've done a variety of programs.

"But there are a lot of socioeconomic reasons that there are issues at the border. You've got, on the Mexican side, historical underinvestments in solid waste cleanup and wastewater treatment facilities."

The Tijuana River flows into an estuary that acts as a natural border between the two countries. The river is in turn bisected by the border wall, which was reinforced beginning in 2008. To do so, the United States razed entire mountaintops and used the earth to fill in gulches and canyons, without paying much attention to long-term erosion concerns. That erosion also contributes to the contamination.

Researcher Oscar Romo is passionate about preserving the Tijuana River Valley. He heads Alter Terra, a binational group that focuses on environmental conservation through infrastructure projects in the San Diego-Tijuana region. He's currently setting up weather stations in Tijuana neighborhoods to track the water flow in the upcoming El Niño.

Romo said while cleanup campaigns look nice and make people feel good, they don't help as much as focusing on, and finding solutions for, the underlying, structural reasons for water pollution.

"NAFTA brought a lot of development and a lot of people from other regions of Mexico, who don't recognize the friendship that these two communities have, and they don't care," said Romo.

"So partially it's education, partially it's attitudes, partially it's geographic conditions, and then on top of that, the [U.S.] EPA used to have a healthy funding system to help Tijuana and other border communities deal with wastewater issues and pollution that has been reduced to almost nothing."

Cal EPA's Aimee Barnes said that tangible positive changes are happening on the border.

"I think we continue to do the best we can to coordinate - we're lucky to have really great partners on the Mexican side of the border who are very enthusiastic about addressing these problems," Barnes said.

"But we're all just challenged with the inevitable challenges that lots of governments face: limited resources to address all of these problems all at once."