"The IDF does not aim to inflict damage to civilian infrastructure and strikes are conducted exclusively on the grounds of military necessity and in strict accordance with international law," a spokesperson said.
"The IDF most certainly does not use water, or any humanitarian resources, as a weapon of war."
It argued Hamas regularly hides militants and stockpiles in places such as water plants and wells.
"The IDF is locating and destroying these terror infrastructures, which have been discovered, among other places, within and near the water facilities in question," the spokesperson said.
While not denying the damage and destruction to facilities across Gaza has been extensive, the IDF insisted it was working to allow repairs to be undertaken