SANDPOINT — The Idaho State Department of Agriculture’s decision to withhold some of the funding for treating Eurasian milfoil infestations in the Pend Oreille with herbicides boils down to effective use of dwindling funds.

“As it’s been every year — and of course more so as money for this project runs out — we have prioritized treatments. Treatments are also based on their efficacy and expectation of success,” ISDA spokeswoman Pamm Juker said on Wednesday.

Bonner County officials were advised earlier this week that ISDA was unwilling to fund the treatment of 334 of the 687 acres of exotic milfoil infestations either because they were too small or they were located in areas of deep water with higher water flows.

Nearly all of the nearly 40 sites excluded for funding are located in the Pend Oreille River west of Dover. Funding for treatment sites in Lake Pend Oreille stayed largely intact.

Officials from ISDA parsed through the county’s application for milfoil grant funding and redlined sites where previous treatments have been less successful due to depth and flow factors.

“We went through each individual site and because of the reductions in the funding and because of the public expectation that it be effectively and efficiently utilized, we made recommendations that we thought were appropriate,” Matt Voile, ISDA’s noxious weed program manager, said on Wednesday.

On Thursday, Bonner County officials met with Tom Woolf, ISDA’s aquatic plants program manager, to further discuss the funding issue.

Woolf told county commissioners and local weed managers what many critics of the herbicide program have believed all along — total eradication of invasive milfoil in the Pend Oreille is impossible. Woolf said the milfoil will continue to flow into the system from the Clark Fork River and the herbicides’ contact time with plants in deeper, swifter water is too insufficient.

A U.S. Army Corps of Engineers dye tracing study and limited success with treating river infestations supports ISDA’s change in philosophy, Woolf said.

“Eradication in this system isn’t going to happen,” he said. “For the Pend Oreille system, we need to be smarter about how we treat.”

But Brad Bluemer, the county’s noxious weed superintendent, did not agree past treatments in the river were ineffective and questioned the wisdom of ISDA’s decision “to walk away and leave half of it in the river.”

Commissioner Lewis Rich said he has long been suspicious of claims that milfoil in the Pend Oreille could be eradicated.

“Why didn’t they figure that out from the get-go?” asked Rich.

Commissioners urged ISDA to work more closely with the county and Woolf encouraged the county to submit amended treatment requests for additional consideration.