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?

"One of my favorites is this one here," says my host, Senior Wildlife Forensic Specialist Jeff Rodzen, "we have a bird who choked to death on the head of a lizard." Hmm. A favorite? Maybe compared to the others lining the wall: jars filled with parasitic worms, a tule elk fetus, a see-through rabbit where you can see every bone.

Add in the bighorn sheep skull among the modern equipment, and the paws sticking up in the back of the evidence and it made for a surreal day of reporting.

Welcome to the autopsy and necropsy room at the California Fish and Game office in Rancho Cordova, about 12 miles east of Sacramento. This is the place where blood and hair and small fibers from wildlife crime scenes are DNA-matched for all the poaching cases in California.

This is a fascinating place, if a little macabre. And it was the starting point for a QUEST radio story that had many more story lines than I could possibly pursue in one feature.

• I learned about a canine program designed to track down poachers, and an offshoot of that program that actually sniffs out invasive species like Quagga mussels.
• I found out how dangerous the job of Game Warden actually is, and the reasons it’s so hard to recruit new officers.
• And I found out how complicated poaching can become, and how endemic it is in California.
• I discovered there’s a subculture of poaching.

Some poachers hit the country backroads late at night, right after the bars close, and Game Warden Todd Tognazzini said those are the easier ones to catch. But the ones who are good at it use sophisticated communications equipment, night-vision sights on their guns, and small, strong flashlights to stun wild pigs or deer into standing still. This is called "spotlighting." Some poachers will black out their brake lights, run on roads without headlights, and use other ingenious ways to keep a low profile while they illegally hunt wild animals.

Game warden is one of the most dangerous law enforcement jobs around– after all, you're going into a remote area, with no backup, to confront people who are carrying guns and knives. Would any urban police officer do that? There is a dearth of game wardens in California, partly due to decades of budget cuts. Last thing I found: The newest high-tech method of tracking down poachers is actually pretty low-tech. Dogs. A new canine program helps game wardens find illegal animal kills. Not surprisingly, poachers hide their contraband, and it's not easy for game wardens to find it. Lieutenant Kristie Wurster is stationed in Alpine County, near Placerville. She’s one of 18 wardens in the canine-training program, and she uses her dog Wrigley to sniff out illegal fishing and hunting. .

Wurster estimates the dog saves about 800 man-hours of work a year. "We are so small in numbers and we just tip the iceberg of how much poaching is going on," she says. "That’s why I’m so excited about the program, to have another set of eyes and ears – and nose – to be able to detect the issues."

Listen to the "Wildlife CSI" Radio report online, and check out our photo set on Flickr which includes: photos of a game warden at work tracking poachers in the foothills of southern Monterey County, as well as deer, boar, abalone and other illegally killed animals.