The stream looks like a waterfall, springing from the shoreline cliffs at the edge of Stanford’s Hopkins Marine Station in Pacific Grove. It flows over quartz-streaked granite rocks, broken abalone shells and slippery clumps of green algae, and into the marine reserve that urchins, otters and cormorants call home. The state designated the Hopkins Marine Life Refuge in 1931 primarily because scientists were using it for research, and to this day marine station staff take great pride in its stewardship.

But the stream isn’t a waterfall; it’s an outfall pipe spouting seawater. The Monterey Bay Aquarium pumped the water from the bay and routed it to Hopkins next door, where it flowed through tanks housing native marine species before discharging into the reserve. Likewise, the Aquarium flushes local seawater through its tanks before returning it to the bay.

Yet the state is giving both Hopkins and the Aquarium major headaches—and dents in their pocketbooks—by making them prove their seawater discharge won’t harm the marine ecosystem. Since 1983 the California Ocean Plan has prohibited the disposal of waste into Areas of Special Biological Significance such as protected marine reserves. But until recently, the water control boards have looked the other way while ocean research institutions dumped seawater containing specimen feces into protected areas.

“The regional board always viewed it as a pretty minimal discharge and not something that we were going to regulate,” says Harvey Packard of the Central Coast Regional Water Quality Control Board. But as more national attention focuses on declining ocean health, regulators are making more of an effort to hold research institutions accountable to state and federal water laws. In 2001 regulators revised the California Ocean Plan to include stricter protections for Areas of Special Biological Significance. Soon after, the state water board zeroed in on cities whose storm water runoff entered protected ocean areas and research institutions dumping seawater into marine reserves.

“We’ve had to spend a huge amount of money to show that we’re not doing anything.

In February 2006 the regional water board sent letters to the directors of Hopkins and the Aquarium, instructing them to apply for an exception to the California Ocean Plan if they want to keep discharging circulated seawater into the bay. To get the exception, they must prove that their outfall doesn’t compromise the marine reserve’s health—or that the seawater cycled through their tanks shouldn’t count as waste.

“If it’s just pure seawater, the state board would not consider it waste,” Packard says. “But if there’s fish excrement in it, it could be considered waste.”

The task is daunting for both institutions, but it hits Hopkins harder. While the Aquarium has an annual revenue of almost $45 million and more than 400 staff members, Hopkins works with a budget of less than $4 million per year and seven staffers, plus 10 research faculty. Both institutions submitted their applications for seawater discharge exceptions in August, and Packard expects the state water board to complete its review within the next few months.

According to spokesman Ken Peterson, the Aquarium has dedicated five staff positions and more than $200,000 to improve its seawater discharge system in compliance with state regulations. The expense puts some strain on the budget, but “we’re able to handle a project of this magnitude,” he wrote by e-mail.

Hopkins, on the other hand, is struggling. Sitting in the cramped office that he sometimes shares with two poodles, HMS Director George Somero explains that the station has already spent $79,000 responding to the state’s concerns—including extensive water testing, marine life inventories, legal counsel, and pipe re-engineering to separate storm and seawater systems and reduce the number of outfalls. And that doesn’t take into account the significant staff time that Somero and others have devoted to the matter.

“We’ve had to spend a huge amount of money to show that we’re not doing anything,” he says. “It’s been quite disruptive to our activities.”

Somero says he’s confident that Hopkins’ seawater discharge poses no threat to the marine reserve because the piping system is carefully controlled. Every day, the Aquarium pumps 2.6 million gallons of seawater from an intake 1,000 feet offshore. Most of that circulates through the Aquarium before returning to Monterey Bay, but roughly 140,000 gallons divert to three storage tanks on Hopkins grounds. With gravity’s help, that water flows into the station’s outdoor aquarium and tanks in four buildings, where it passes once over Hopkins’ specimens—mainly sea urchins, snails, mussels and squid—before draining into three pipes that discharge into the Hopkins State Marine Reserve.

Station staff add no chemicals, antibiotics or metals to their tanks, and they dump water that comes in contact with exotic species down the sewage pipes. So seawater returns to the bay almost the same as it came—except with a little additional sea critter poo. Somero estimates that resident specimens produce no more than .6 pounds of excrement daily, which is about as much feces as a single 100-pound harbor seal produces, along with about 1.2 liters of urine, every day. Add to that the daily excretions of resident sea otters, geese and tens of thousands of mussels, snails and fish in the marine reserve, and the quantities of naturally occurring excrement make the turd-load in the Hopkins seawater discharge seem negligible. “These animals are going to pee in the water anyway,” Somero says. “It’s not like being in our tanks is going to change anything.”

Somero hopes the state and regional water boards will agree, because the 115-year-old marine station could shut down if they don’t. According to Somero, 90 percent of the station’s research depends on the seawater system, and alternatives to the current discharge scheme—such as re-circulating the water or dumping it outside the marine reserve—are impractical and expensive.

“Our ability to sustain our programs in education and research depends absolutely on the continued operation of our seawater and aquarium systems,” he wrote in his August response to the regional water board.

Luckily, the state seems willing to cut research institutions a break. The water board has already granted seawater discharge exceptions to Scripps Institution of Oceanography and the USC Wrigley Marine Science Center, but at an expense that makes Somero cringe. Scripps, which discharges into the San Diego Marine Life Refuge, will spend about $10 million on compliance during the five-year permit cycle, according to Kimberly O’Connell of the UCSD’s environment department. That’s likely more than Hopkins can afford.

Shutting down Hopkins Marine Station would deal a heavy blow to California’s marine reserves, Somero says, because Hopkins scientists help inform public policy decisions about how to structure and manage them. Somero’s assistant, Joe Wible, notes the irony. “Our scientists are the ones who identified the Areas of Special Biological Significance,” he says, “and now it’s coming back to bite us.”