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In the long-running battle over the Boston waterfront, the latest round goes to the side calling for less, not more.

A Suffolk Superior court judge Friday allowed lawsuits challenging new zoning that would enable developer Don Chiofaro to build a massive waterfront tower to go forward to trial. Judge Brian Davis rejected motions to dismiss the suits filed by the Conservation Law Foundation and residents of the Harbor Towers condo complex challenging how the state handled the new zoning, setting up a legal showdown over what, exactly, can be built along the edge of Boston Harbor.

The Conservation Law Foundation has said the zoning does too little to protect public access to the waterfront while allowing too dense development there, and charged then-environmental secretary Matt Beaton with violating state law when he approved it.

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“It is unacceptable that this plan allows developers to buy their way out of regulations they don’t like,” CLF senior counsel Peter Shelley said in response to the judge’s ruling. “The public’s right to access the waterfront has been guaranteed for generations, and officials have singlehandedly undermined that right. The municipal harbor planning process is broken, and we’re looking forward to proving it in court.”

Residents of Harbor Towers, too, sought to block the zoning and, by extension, Chiofaro’s project, which would sit next door on East India Row, near the New England Aquarium. They’ve argued the proposed 600-foot tower is simply too large for a site so close to the waterfront, and said they look forward to making their case in court.

“The state’s regulations require waterfront development to be ‘relatively modest,’ ” said spokesman Tom Palmer. “The court’s ruling allows us to make the case that a 600-foot, 900,000-square-foot tower is anything but modest and will harm public access to the waterfront.”

Reached Friday evening, Chiofaro said he hadn’t yet seen the ruling and had no immediate comment.

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While the zoning particulars were drawn up by the city of Boston, they were approved by the state because of the area’s proximity to protected tidelands. The state and Chiofaro sought to have the suits dismissed.

The ruling is another twist in the long, long saga of Chiofaro’s tower, which the veteran developer first proposed on the site of the Boston Harbor parking garage in 2007.

Since then, he has tangled with former mayor Thomas M. Menino, the New England Aquarium, various neighbors, and CLF. Boston Mayor Martin J. Walsh and then Beaton finally approved zoning for the area — which would allow for a tower of that size — in 2018. Then came the lawsuits.

Meanwhile, according to people familiar with his plans, Chiofaro has quietly been prepping to file for what he has previously said would be a landmark office and hotel tower that would transform a central part of the downtown waterfront and skyline.

Just Thursday, the Boston Planning & Development Agency nailed down final details of the zoning plan, which would clear the way for Chiofaro to do something what he hasn’t done over the course of more than a decade: file official buildings plans that would kick off a public review. People familiar with the project have said that could happen by the end of this year.

A lengthy trial that is now allowed to move forward, though, could mean nothing gets resolved for some time.

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Tim Logan can be reached at tim.logan@globe.com. Follow him on Twitter at @bytimlogan.