The California Coastal Commission was reluctant to approve Santa Barbara’s repair and maintenance permit for the desalination plant since it has concerns about the project’s seawater intake, but commissioners really had no choice.

Santa Barbara’s 1996 coastal development permit for the Charles E. Meyer Desalination Plant is still valid, which means the city doesn’t have to go through another coastal development permit review.

The plant has been in standby mode ever since and the city has to spend upwards of $40 million to get it operational again, but the reactivation doesn’t count as a new or expanded project.

Instead, the Coastal Commission met to discuss a repair and maintenance permit for the city, which outlines rules for putting seawater pumps back into the ocean and making system upgrades for the 25-year-old system.

The desalination plant pumps in seawater from the open ocean intake structure, located 2,500 feet offshore, and the waste is mixed with the discharge from El Estero Wastewater Treatment Plant, located 8,720 feet offshore.

Many people are frustrated over the open ocean intake, and even the Coastal Commission staff said that the city would be forced to study a subsurface seawater intake structure if it was a new facility instead of an existing one.

“We have no choice here,” commissioner Mary Shallenberger said. “We’re doing this under duress, and I’m not happy about it.”

There is no baseline study from the 1990s, no study of the impacts from the previous time the desalination plant was operating and therefore no way to assess the cumulative impacts, she said.

“So I’m very frustrated by this but we’re stuck, legally,” Shallenberger said. “We know so much more now than we knew in 1996. This permit as written in 1996 I believe would never pass the commission in its current form.”

The city’s description of its offshore work, including the replacement of pumps, electrical systems and screen components, is within the scope of the 1996 permit approval, district manager Robert Merrill said. The use of heavy equipment on beaches and in the ocean requires the repair and maintenance permit, which the Coastal Commission approved Friday.

Santa Barbara should be studying subsurface intake systems and the environmental impacts of an open ocean intake, argued environmental activists Susan Jordan of the California Coastal Protection Network and Kira Redmond of Santa Barbara Channelkeeper.

They pushed hard for a subsurface intake study at the Central Coast Regional Water Quality Control Board hearing last week and the board made the study a mandatory condition of the city’s National Pollutant Discharge Elimination System permit.

“For a city that prides itself on its environmental ethic, it should not be sticking its head in the sand. The only thing in the sand should be a subsurface intake,” Jordan said in a letter to the board.

Shallenberger called it “unconscionable” that the analysis wasn’t done before and urged the Coastal Commission to send a letter to the Regional Water Board, asking it to require more in-depth environmental studies and to make them available to the public as a condition of future permits for Santa Barbara.

Coastal Commission Vice Chair Jana Zimmer pointed out that the city isn’t required to implement an different seawater intake even if the feasibility study recommends it.

DJ Moore, a legal representative for the city with the Latharn & Watkins firm, confirmed it, saying the city’s vested rights under existing permits mean Santa Barbara isn’t required to implement recommendations from the study of intake alternatives.

Unless the city promises otherwise, “essentially the city may continue with an open ocean intake forever,” Zimmer said.

“I just want to go into this with my eyes open.”

Santa Barbara Mayor Helene Schneider said the City Council views desalination as an “absolute last resort,” but the city faces a water shortage even after residents have cut use by more than 20 percent.

With the ongoing drought, Santa Barbara expects to start up the facility producing 3,125 acre-feet per year, or about 1 billion gallons. If there’s no rain in the coming 2015-16 winter, the city could increase the capacity to 7,500 acre-feet per year.

The facility is expected to be ready for production by fall 2016, according to the city.

Council members haven’t decided on the scope of the intake structure alternatives yet and talking about issues of impingement (larger animals getting stuck against intake screens from the flow of water) and entrainment (smaller organisms getting pumped into the intake and treatment system) will likely be part of that analysis, she said.

This Coastal Commission permit approval is the last regulatory hurdle from an outside agency, Schneider told Noozhawk. The city doesn’t plan to award a design/build contract until June, she added.

“I think we all want it to rain but if it doesn’t, we need some water,” she said.

Noozhawk news editor Giana Magnoli can be reached at gmagnoli@noozhawk.com. Follow Noozhawk on Twitter: @noozhawk, @NoozhawkNews and @NoozhawkBiz. Connect with Noozhawk on Facebook.