The paddling pools include the Fairy Dell in Skegness and the ones at Sutton on Sea and Mablethorpe.
East Lindsey District Council say they are disappointed they will not be able to open the paddling pools but explained more work is needed before they will be safe to use.
A statement reads: "It is with great disappointment to the Council that it won’t be able to open its three paddling pools at Skegness, Sutton on Sea and Mablethorpe for the bank holiday weekend.
"Having started to fill the pools in good time, their extended 20 month closure due to Covid restrictions has resulted in far more extensive work being necessary to their pumping and filtration systems.
"The work, that can only be identified upon filling, is underway, however, until the water can be fully treated, the pools cannot open as the safety of pool users is paramount.
"The Council hopes to be able to open all of its paddling pools shortly after the Bank Holiday and fully appreciates the disappointment their delayed opening may cause.
"The closure of each pool is well signed and the Council hopes that eager residents and visitors avoid any risks by respecting their temporary closure."