San Diego Unified School District Superintendent Bill Kowba will step down on June 30, he announced at tonight’s school board meeting.

Kowba led the district for three years. Prior to his selection as superintendent, he served as the district’s chief financial officer for four years. His contract expires on June 30 and he is leaving on good terms with the school board. At the meeting, his announcement was met with a standing ovation.

“It is after much reflection and consultation with my family and with great mixed emotions that I make this decision,” Kowba said at the meeting. “I want to thank you for the honor and privilege of leading this outstanding large urban educational institution.”

My former colleague Emily Alpert profiled Kowba in 2010, dubbing him an “accidental superintendent.” Here’s a snippet from that piece:

Bill Kowba is something of an accidental superintendent. He has no long line of school districts to point to. He has never taught a class. The former Navy man was reluctant at first to throw his hat in the ring.

But after twice being tapped as the interim superintendent of San Diego Unified, after the departures of Carl Cohn and Terry Grier, Kowba was praised over and over for his steady hand and honest leadership. For a school district that seems shell-shocked by the revolving door of three superintendents in five years and a barrage of budget cuts, Kowba has been reassuring and trusted.

“Here is a guy who has been in the seat a couple of times and keeps coming back when others have fled,” said Michael Casserly, executive director of the Council of Great City Schools, who recommended Kowba for the job for his even keel. “He strikes me as a keeper.”

The five-member school board offered Kowba effusive praise after his announcement Tuesday.

“San Diego Unified has gone through tumultuous times over the past two decades,” said Board President John Lee Evans. “We congratulate Superintendent Kowba for the stability that he has finally brought to this district.”

Trustee Richard Barrera agreed.

“I just want to thank Bill Kowba for being a role model that any of our young people could look up to for how to live your life in a way that makes a difference to other people,” Barrera said.

Kowba leaves behind a district still struggling with significant financial problems.

Next year, the district faces a projected deficit of about $86 million. To close that deficit, the school board has resorted to selling off district real estate and not hiring teachers to replace those that retire or quit, a move that will result in swelling class sizes.

And, as we pointed out in this story last week, the district won’t be saved by Proposition 30, which was pitched as something of a panacea for the state’s education funding woes. Rather, much of the new tax revenue from Proposition 30 will increase San Diego Unified’s operating costs, since it will be used to give teachers and other staff across-the-board raises they agreed to defer in the past. It will also cancel unpaid days off, which will lengthen the school year..

Evans said the school board would attempt to replace Kowba before his contract ends.

Will Carless is an investigative reporter at Voice of San Diego currently focused on local education. You can reach him at will.carless@voiceofsandiego.org or 619.550.5670.

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Will Carless was formerly the head of investigations at Voice of San Diego.

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