LONGVIEW, Wash. — Dalton Fry cast a finely meshed net into the murky Cowlitz River. He waited a few minutes, then hauled it in and poured the contents into a glass jar. There swam dozens of smelt larvae, their eyes protruding from barely visible bodies.

“There’s probably 100 in there, no problem,” Fry, who works for the Cowlitz Indian Tribe, said last week.

Seals swimming nearby off the boat launch at Gerhart Gardens indicated that adult smelt were cruising the river, too.

This time of year, smelt larvae and adults are coursing through lower Columbia watershed. The run apparently lasts longer and the fish are swimming farther up rivers than biologists previously believed.

There are indications that the run is rebounding, too.

But that doesn’t mean dipping for the once-plentiful fish will be reinstated any time soon. Two years ago, smelt were listed as threatened under the federal Endangered Species Act, and the Washington and Oregon departments of fish and wildlife haven’t allowed sport or commercial dipping since.

Researchers for Washington, Oregon and the Cowltz Tribe are in the second year of research projects about smelt and still have years of study to do before developing a reliable way to count the oily fish.

The states are focusing on smelt in the Columbia River while the tribe, fittingly, is doing much of its work in the Cowlitz River.

For decades, fish managers admitted that they didn’t know much about smelt — and didn’t really need to.

The fish kept returning every year in big enough numbers for dippers to fill their buckets. When a major smelt run appeared in February or March, dippers would line the banks of the Cowlitz River into the wee hours, creating so much noise that Kelso finally asked the state to prohibit dipping after 10 p.m.

However, smelt runs on the Cowlitz and other local rivers started to falter in the 1980s, and the last decent run was in 2003. Smelt were also faltering on coastal rivers from California to British Columbia. In 2007, The Cowlitz Tribe petitioned to have the fish listed under the federal ESA, and the National Marine Fisheries Service listed them as threatened in March of 2010.

Before the listing, “there was no money to monitor smelt because it was just a bait fish,” said Chris Wagemann, a WDFW smelt researcher.

But where there’s an endangered species, there’s federal research money. In 2010, NMFS awarded $1.6 million to the Oregon and Washington DFWs and another $811,306 to the Cowlitz Tribe for three years of research. The funding for next year’s research, however, has been cut by about 70 percent.

A ‘tremendous spawning area’

During the smelt run, tribal workers leave devices similar to crayfish traps in rivers overnight to capture adult smelt. They also use plankton nets to catch larvae and eggs.

“We’re trying to establish the upstream extent they use for spawning,” said Craig Olds, lead smelt biologist for the tribe.

On the Cowlitz, Fry can leave a net in the water for only a few minutes. “Your whole net will be full of sand if you do it too long,” he said.

Despite the river’s murkiness, the water samples taken at Gerhart Gardens were rich with smelt larvae. “This is a tremendous spawning area,” Olds said. “We don’t know how far up, but it probably extends all the way to the Toutle River.”

Smelt run hard to count

One of the WDFW researchers’ goals is developing an accurate method of measuring the size of the smelt run in tons, based on the number of eggs and larvae.

In past years, the best gauge was the amount of commercial catch, which was partially influenced by the market for bait and zoo feed. But with all smelt fishing prohibited, commercial landings are no longer an option to measure the run size.

With salmon and steelhead, biologists can observe spawning sites in tributaries and count the number of fish returning to hatcheries and crossing Columbia River dams. Hatchery salmon smolts are implanted with tiny wire tags that scientists can track out into the ocean.

But smelt spawn out of sight at the bottoms of rivers and don’t reach hatcheries — and their larvae are obviously too tiny for wire tags.

“There’s no run for us to go out and count,” said Phillip Dionne, a WDFW researcher. “The fish are small. We can’t handle them. There’s not fisheries on them anymore.”

The Washington DFW has a three-person smelt research team focusing on sampling eggs and larvae in the Columbia River near Cathlamet. Several times a week, Wagemann heads out onto the river on a boat and drops a plankton net overboard for three to five minutes.

Back at the lab, workers pour water samples into dishes and peer at them through a magnifying glass. “Our technicians spend hours and hours and hours and hours looking through microscopes” to count the eggs and larvae, Dionne said. The Cowlitz Tribe has a similar lab.

Another part of the research is dipping mats that smelt eggs adhere to into the river.

Factors in the population equation are the male-female sex ratio and how many eggs a female produces, which is thought to range from 20,000 to 60,000. “There’s still a lot of questions about how confident we are about the sex ratio and the fecundity,” Dionne said.

The Northwest Fisheries Science Center at Point Adams near the mouth of the Columbia is testing the use of sonar to measure the smelt run, similar to the way commercial fishermen use the technology to find schools of herring.

Biologists have been surprised to learn just how early smelt begin to appear in the Columbia River. They used to think that a pilot run of smelt appeared in December, followed by the main run in February, “typically around Super Bowl time,” Wagemann said. However, the biologists found smelt larvae in the Columbia last December, which means the smelt would have spawned about 30 days earlier. Next year, they’ll start searching for larvae in November.