Floodwaters caused by a two-day rainfall total of eight inches surged through streets in the capital Thursday and closed some schools and the international airport.
Red Cross spokesman Adolfo Beteta said 18 people were rescued from flooded homes in the western part of the city. No deaths were reported.
Several schools canceled classes on Wednesday and did not open Thursday because there was water in the buildings.
A weather service broadcast warned citizens to maintain a state of alert because heavy rains were expected to continue.