SANTA ROSA -- Santa Rosa is appealing new rules regulating the discharge of treated wastewater from its Laguna Wastewater Treatment Plant, arguing that guidelines issued last November could undermine existing efforts to recycle the vast majority of treated waste for agriculture and electricity and ultimately lead to higher ratepayer costs.

The city received formal notification this month that the State Water Resources Control Board, a high-level water regulator, had received the petition following initial filing in December. The document contends in part that the board's North Coast division went too far in setting a "no net loading" policy regarding the release of phosphorus into the sensitive habitat of the Laguna de Santa Rosa.

It also questions measures that the city claims would make the treated wastewater it sells to farmers for irrigation less cost-competitive versus potable water, noting that those costs currently stand at around 5 percent less.

"Our recycled water system in general is renowned in the state," said David Guhin, the city's utilities director. "We're very concerned that these additional restrictions are going to discourage people from using that product."

The new permit, effective as of Feb. 1, requires that the city take measures elsewhere in the watershed to lower the overall input of phosphorus into the Laguna. The arrangement allows the city to "bank" those credits for future use, a system that Mr. Guhin said is the first of its kind in California.

Yet concern remains for the long-term practicality of such an arrangement, as well as the city's opinion that a small amount of discharge into the Laguna would have no significant effect, he said.

"We've hit all the low-hanging fruit, so we're worried about finding projects going forward," Mr. Guhin said. He described current projects focused on runoff from roads and dairies, and that "as the projects run out and we have to spend more to offset a pound of phosphorous, it's going to start affecting ratepayers."

Mr. Guhin estimated the current cost of mitigation credits for one ton of discharged phosphorous at around $30, amounting to around $100,000 per year. That number could balloon if mitigation sources within the watershed become harder to find, he said.

The petition claims that the city acted in good faith by investing five years and approximately $1.5 million in those mitigation efforts. Yet it argues against the policy in general, vying instead for a reasonable limit that would eventually follow a "total daily nutrient load" limit for the Laguna that is currently under study.

"We feel there is an acceptable level," Mr. Guhin said.

The city estimates that it contributes between 1.8 percent and 2 percent of the total load of phosphorous in the Laguna on average, according to the petition.

The North Coast Regional Water Quality Control Board, the local regulatory division, approved a new wastewater permit for the Laguna plant in November 2013. The permit followed a year of research concerning the Laguna itself, and is part of a regular five-year cycle for wastewater plants throughout California.

Santa Rosa received additional attention due to the sensitive nature of the Laguna habitat, which is the designated area for treated wastewater discharged from the plant, said Mona Dougherty, senior water resource control engineer at the North Coast water board. Phosphorus exists naturally, but can prompt runaway algae growth and subsequent depletion of water-dissolved oxygen in high concentrations.

"We think we handled all the water quality issues in a fair and equitable way, based on sound science," Ms. Dougherty said. "The permit for Santa Rosa has some more additional science and research because it deals with an impaired water body."

The Laguna de Santa Rosa is a large wetland habitat and tributary of the Russian River, part of a 254-square-mile watershed encompassing the entirety of the Santa Rosa plain. It is home to hundreds of species and a common stopover for bird migrations, subject to runoff from Santa Rosa, Windsor, Rohnert Park, Cotati, Forestville and Sebastopol, according to the nonprofit Laguna de Santa Rosa Foundation.

The city's petition points to the plant's recent history in recycling the vast majority of its wastewater as in line with the state board's broader goals, arguing that the permit as structured would run counter to those efforts by diverting resources to phosphorus mitigation. The plant serves around 225,000 residents in Santa Rosa and surrounding municipalities, and discharged no water at all to the Laguna in 2013 and 2009. There were only marginal discharges in the intervening years, the city said.

That water instead goes to recharge the aquifer at the Geysers geothermal field in northern Sonoma County and to irrigation for agriculture and a handful of other properties. Discharge becomes necessary in some conditions, including ongoing and heavy rainfall.

"The last thing we want to do is discharge. But it's that critical safety valve you need to have on the system," Mr. Guhin said.

The plant has been in operation since 1968, and was most recently upgraded through a $49 million bond issue in 2008. It is one of the largest wastewater facilities in the region, able to handle high-strength waste and around 21 million gallons per day.

The state board has yet to schedule its review of Santa Rosa's petition. If dismissed, ratepayers would have another two years before a new rate schedule reflected any impacts, Mr. Guhin said.

The Santa Rosa City Council this month approved two 5 percent increases in fixed water charges over two years, along with two 3.5 percent increases over the same period in wastewater fees.