Every year, millions of fish make a strange and harrowing detour through the Skinner Fish Facility, part of the State Water Project's facilities in the Delta.

In my last post, I wrote about my visit to the Banks Pumping Plant, whose giant pumps slurp water from the Delta to help quench California's thirst. As the volumes of water are sucked up, both resident and migrating fish come along for the ride. The Skinner Facility, in operation since 1968, was built to protect fish from being killed at the pumps–an effort that sadly is not as successful as one would hope (more on that below).

I was amazed to learn there is a whole art and science to fish screens, which range from physical barriers–called positive barriers–like perforated plates or wire mesh, to behavioral barriers like sound, light, or other stimuli aimed at keeping fish away. Well-designed screens minimize both entrainment (fish being pulled into the pump or diversion) and impingement (fish being trapped or injured against the screen itself due to water velocity).

Both physical and behavioral barriers are used at the Skinner Facility. Fish being pulled toward the pumps first encounter a trash rack that diverts many bigger fish, along with floating debris. Next, fish encounter a large, v-shaped array of metal louvers. The louvers create turbulence that functions as a behavioral signal, encouraging the fish to swim away into bypass pipes that function, as our tour guide put it, like "a big vacuum system."

From the bypass pipes fish travel to another set of louvers and pipes, concentrating them into a smaller volume of water, and then into holding tanks in a nearby warehouse. Giant, suspended cone-shaped buckets are used to periodically sample the fish, which are identified, counted, and measured. Some 90 species turn up in the facility, including Chinook salmon, steelhead, white sturgeon, and delta smelt. (I asked our guide if delta smelt really do smell like cucumbers. He confirmed it. In fact, when a school of smelt comes through–an event that has become rare–the warehouse smells "like a salad.") When enough fish have been collected, they are loaded into trucks and driven back to the Delta.

Here's the rub. Many fish caught in the pull of the pumps are lost to predation before even reaching the screening facility. Then, the facility does not effectively screen fish smaller than about 1.5 inches, meaning that littler, less powerful species and juveniles are still vulnerable to the pumps. For the fish that make it to the holding tanks, the process is such a trauma–with big and little fish squashed together in the tanks, buckets, and trucks–it's no surprise there are casualties; in fact, the delicate delta smelt often do not survive. And even for fish that make it through the entire process and out the other end, there's a final, fatal hurdle: the trunks routinely dump salvaged fish at the same locations, where more predators have learned to cluster for a free lunch.

Scientists agree that the loss of fish at the huge state pumps–and other pumps and intake pipes throughout the Delta–is a major contributor to plummeting populations. How much water we use makes a difference: The higher the export rates, the more fish are entrained. There also is broad consensus that more state-of-the-art fish screening facilities are needed. That could come with a hefty price tag. But with our fish disappearing, can we afford not to invest in their survival?

photo courtesy of the San Francisco Public Utilities Commission

Those spills got a lot of coverage, including by KQED, so our question was a little broader. Were those spills an anomaly? (Answer: No, they were big, but not unusual.) And how does this happen in as eco-conscious a place as the Bay Area? What would it take to stop it?

The two Mill Valley spills seem to have resulted from a few different problems: overwhelmed capacity, failed alarms, operator error, and probably other factors, too. But the underlying cause is the same, and it’s true of many sewage systems in the Bay Area: These systems — the pipes, the digesters, the pumps – are reaching the end of their useful lives. (Some of the older clay pipes were built in the 1850s!) Few cities are jumping to do the necessary upgrades, and who can blame them? What’s less sexy than an expensive, disruptive construction project that takes place mostly underground, out of sight?

Still, as we say in the piece, we’ve done it before. Those who lived in the Bay Area before the 1970s may remember the stench of raw sewage drifting up through the car window as they crossed the Bay. Thanks to the Clean Water Act of 1972, the Bay is vastly cleaner than it used to be and there are far less spills.

So what will it take to get cities to pony up the cash this time around? Baykeeper is taking the issue to the courts – you can read more about their Sick of Sewage campaign here: http://www.baykeeper.org/

You may listen to the "Sewage Happens" Radio report online, as well as find additional links and resources.

Amy Standen is a Reporter for QUEST and Radio News at KQED-FM.