Heavy rainfall in the Paphos district kept the fire service busy overnight while a yellow weather warning remained in place on Monday morning.
At 5.52 on Monday morning the fire service in Paphos were told about flooding at the entrance of Polis Chrysochous gymnasium.
Fire fighters were able to remove the water and children were able to attend school as usual.
A little earlier, at 4.20am, water was pumped from another building.
Some small damages were also reported.
Police warned due to the rain there have been landslides on the Paramytha to Gerasa road in the Limassol district.
Roads are slippery and drivers are urged to be careful, especially where water has accumulated.
A new low pressure system which is expected to last at least until Wednesday is causing the rain and the met office on Sunday issued the yellow weather alert.
On Monday and Tuesday rain, hail and storms are expected in all areas of Cyprus.
Temperatures will reach 20C on Monday but are expected to be lower in the following days, during which some snow may fall in the higher mountain regions.