Rain water has been leaking into Blackbaud’s Daniel Island headquarters for years.

But now the problem has gotten so bad that some employees must move into a nearby building while the leak is fixed, the software firm said in a federal regulatory filing.

Under the terms of the deal, Blackbaud’s landlord, a company controlled by Blackbaud founder Tony Bakker, will cover the costs associated with the disruption, including the repairs and more than 10,000 square feet of office space at 146 Fairchild Ave., also on Daniel Island. A Blackbaud spokeswoman declined to comment on the disclosure that was filed Thursday with the Securities and Exchange Commission. She referred all questions to Bakker’s Duck Pond Creek-SPE LLC.

Bakker, who owns the Charleston Battery soccer club, did not respond to a request for comment Friday.

Blackbaud moved into its newly built 235,000-square-foot headquarters at 2000 Daniel Island Drive in 2000, the same year Bakker stepped down as CEO.

It’s unclear when the leaking started, but according to the lease amendment and remediation agreement signed this month, a water infiltration investigation was completed in 2006. It’s also unclear what was done in the intervening seven years, or how long the fix revealed this week will take.

Plans to do exterior repair of the Blackbaud headquarters were dated Sept. 17, 2012, according to the March 22 lease amendment. Under the terms of the contract, no more than 9,000 square feet of the headquarters building can be closed at a time.

“Upon notice from Blackbaud of any continued water intrusion or other defects in completed portions of the Work, construction shall not commence in new portions of the Leased Premises until such defects have been cured,” according to the agreement.

The document didn’t say how much of the building is affected or how many employees will have to move to Fairchild Street. It also didn’t provide an estimate about how much the repairs and other costs will be, but there were hints that they could be quite extensive.

“Alternate non-monetary arrangements reasonably acceptable to Blackbaud shall be made at Landlord’s expense during any closure of the cafeteria and fitness facilities,” the exhibit stated.

Blackbaud is in the midst of other transitions as well.

Almost a year after making its biggest acquisition to date, former Texas rival Convio, Blackbaud is working to integrate its products and personnel.

In January, the company announced CEO Marc Chardon would step down at the end of this year or sooner if his successor is named. The company recently entered into retention agreements with four top executives and hired an executive search firm as part of that process.

Reach Brendan Kearney at 937-5906 and follow him on Twitter at @kearney_brendan.