Department of Water and Power head Ron Nichols on Thursday announced his resignation amid growing financial and administrative controversies at the agency.

Nichols, a former energy and water utility consultant, has been general manager of the nation’s largest public utility for three years. He has taken heat over the rollout of the DWP’s new billing system, which has issued thousands of inaccurate bills and made large withdrawals from some ratepayers’ bank accounts in error.

In addition, the agency has been unable to account for an estimated $40 million in ratepayer revenue spent by two non-profit trusts co-managed by Nichols and Brian D’Arcy, business manager of DWP’s biggest union, the International Brotherhood of Electrical Workers Local 18.

City Controller Ron Galperin on Wednesday said he would seek subpoenas to force D’Arcy to turn over financial records in the case.

In his resignation letter, Nichols said he was leaving for personal reasons. He did not make specific mention of the controversies, and implied that he had expected to depart after Mayor Eric Garcetti took office last year, but wanted to give the new administration time to get settled.

Garcetti, who has made reform of the utility a priority for his administration, has not announced how he plans to fill the post.

“I’m focused on continuing to reform the DWP to cut costs, improve customer service and increase transparency,” Garcetti said in a statement sent to the media that included a copy of Nichol’s resignation letter.

In last year’s race for mayor, Garcetti handily defeated Wendy Greuel and his victory was largely credited to painting her as a lackey of the DWP union.