The Metropolitan Water Reclamation District of Greater Chicago agreed Thursday to pay $95,000 to its former boss, who resigned after an investigation by the agency’s board into an unspecified matter.

David St. Pierre, who made about $292,000 in 2017, resigned effective June 27 as executive director of 2,000-employee, $1.2 billion-a-year government agency.

He’d headed the agency — which treats sewage and wastewater in Cook County, works to prevent flooding and safeguards waterways from pollutants and toxins — since 2011.

Last week, the district announced his resignation without saying why he left. On Thursday, its board approved the separation agreement, which also includes health insurance for six months but still wouldn’t explain St. Pierre’s departure.

Citing a non-disparagement clause in the deal, district commissioner Debra Shore wouldn’t talk about the investigation other than to say it wasn’t over criminal or sexual matters.

David St. Pierre.

David St. Pierre.

Shore said St. Pierre “had both admirers and detractors” on the water district’s nine-member board and that she was as an admirer.

Asked about his resignation and the investigation, St. Pierre would say only, “It was the right time.”

The board investigation was done by Zaldwaynaka “Z” Scott when was a partner in the Chicago office of the aw firm Foley & Lardner before being appointed president of Chicago State University. Scott is a former assistant U.S. attorney who also previously was executive inspector general for the state of Illinois.

Scott didn’t return calls.

The water reclamation district settled lawsuits last year filed six years earlier by environmental advocates that accused it of violating the federal Clean Water Act with its discharges of phosphorous from three of sewage-treatment plants into the Chicago River.

In 2015, the Chicago Sun-Times and the Better Government Association reported the water reclamation district had, for 99 years, been leasing land it owns along the Stevenson Expressway for bargain prices, in some cases to tenants that had been cited and sued over environmental violations. The Sun-Times also reported that the tenants included one that failed to report a 50,000-gallon antifreeze spill.

John P. Murray, who has been director of maintenance and operations, will be acting executive director until a replacement is hired.

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