The Oakland City Council’s recent closed-door vote to drop its lawsuit seeking to block Alameda County from selling its half-share of the Oakland-Alameda Coliseum site to the A’s was a tough win for the team. And upcoming votes could be even tougher.

The vote to dismiss the controversial suit wasn’t unanimous and underscored the challenges that lie ahead for the new waterfront ballpark the A’s hope to have open in 2023 at the Port of Oakland’s Howard Terminal.

“I’m not sure this is going to get done on the A’s timetable. There is still a ton of work to be done,” Councilman Larry Reid said after the vote last week to dismiss the lawsuit that was threatening the negotiations to keep the team in Oakland.

Major League Baseball Commissioner Rob Manfred had told city officials the privately financed Howard Terminal ballpark and the A’s proposed Coliseum development deal were an “all-in-one proposition,” meaning the development would help pay for the new stadium. However, the A’s have never definitely stated that profits from the Coliseum deal would finance the waterfront ballpark.

And when the team tried to buy the county’s half interest in the prime, 155-acre site for $85 million, the City Council moved to block the deal, triggering Manfred to warn them that the city could lose the A’s if they persisted in their legal challenge.

With the MLB deadline of Nov. 15 fast approaching and after meetings between city negotiators and the A’s, council members were given two options by the city’s negotiating team.

Make MLB happy and dismiss the lawsuit “with prejudice,” meaning the legal challenge would go away for good and negotiations would continue with the A’s over the possible sale of the city’s portion of the Coliseum site to the team as well.

Or dismiss the suit “without prejudice” — the city attorney’s recommendation — meaning the suit could be revived if talks with the A’s fell apart.

The council ultimately dropped the suit for good.

City negotiators had told the council that talks with the A’s were going well, and the team and the city “were 90%” in agreement on a possible deal to either purchase the city’s share for $85 million or negotiate a long-term lease, according to council members who did not want to speak on the record because the vote was in closed session.

Mayor Libby Schaaf, City Council President Rebecca Kaplan and Reid all recommended fully dropping the suit.

Councilman Noel Gallo, who wants the A’s to build the new ballpark at the Coliseum site rather than at Howard Terminal, voted against dropping the suit.

“I’m for getting the best negotiated deal for the city, not the best negotiated deal for the A’s,” Gallo said. “The only reason we were getting a good deal was because of the threat of a legal challenge.”

Councilman Dan Kalb, who has said in the past that he could only support a noncompetitive development deal with the A’s at the Coliseum site if the team built the new ballpark there, abstained from voting.

The remaining council members voted to drop the suit entirely.

Those keeping a close eye on the ballpark talks, however, said the monthlong legal squabble is just the first challenge in what will likely be a series of tough decisions by the council in the months to come on the ballpark deal.

Next up will be approval of the environmental impact report on the project, which will lay out transportation needs at Howard Terminal as well as the impacts of the ballpark, hotel and 4,000 units of housing that make up the team’s waterfront plan.

“We look forward to the city’s release of the EIR for our Howard Terminal project in the next month or so, followed by a 45-day public comment opportunity,” A’s President Dave Kaval said.

In a hint of what’s ahead, a coalition of port maritime tenants, unions, businesses and truckers opposed to a waterfront ballpark shot off letters to the city the day before the council voted to drop the suit, renewing the group’s opposition.

“This isn’t just about a baseball stadium,” said Pacific Merchant Shipping Association Vice President Mike Jacob. “The city has a vision of intense housing development near Howard Terminal, with 30,000 residents and another 30,000 fans on game days with no plan to preserve the port’s industrial base.”

But the real test will come when the council deals with the special use tax district it will need to set up to help pay for Howard Terminal infrastructure costs — those could run up to $200 million.

Adding to the drama, the vote to create the special ballpark district will likely come at the same time as voters are being asked to approve a new $148-per-parcel tax to help maintain the city’s deteriorating parks.

It will be interesting to see how voters react when real choices about money are at stake.

San Francisco Chronicle columnist Phil Matier appears Sundays and Wednesdays. Matier can be seen on the KGO-TV morning and evening news and can also be heard on KCBS radio Monday through Friday at 7:50 a.m. and 5:50 p.m. Got a tip? Call 415-777-8815, or email pmatier@sfchronicle.com. Twitter: @philmatier