Authorities installed pumps to bring down water levels, which were 1.7-meters (yards) high in several subdistricts and reached up to two kilometers (more than a mile) inland, but said they expected tides to continue to wreak havoc through the end of the month.
Residents in north Jakarta have grown used to flooding during the monthly high-tide cycle, but Monday's was the worst in memory.
The disaster was blamed on ignored warnings about exceptional 18-year high tide cycles, Jan Japp Brinkman, a flood expert, was quoted as saying in the Jakarta Post newspaper. The situation was exacerbated by a failure to fix a sea barrier that was breached over a week ago.
At least 8,000 houses were flooded and sea water swamped the toll road connecting the capital with the Soekarno-Hatta airport, leaving thousands stranded or trapped in kilometers- (miles-) long traffic, Kompas newspaper said.
Many flights were disrupted or forced to leave with only a handful of passengers, Muhammad Reski, the airport's officer-in-charge, said Tuesday.