Torrential rain has buffeted the capital since Sunday, causing flooding at 52 locations, and claiming two lives, including a sanitation worker who was swept away while taking photos of the flooding for the Jakarta administration.

The atmosphere is already febrile in the city as two gubernatorial candidates prepare to face off in a second-round election in April.

However, despite the dramatic lead up to the February elections - during which the incumbent, Basuki "Ahok" Tjahaja Purnama, was accused of insulting Islam - post-vote surveys revealed religion was a determining factor for only about 8-10 per cent of voters.

It appears voters were more persuaded by candidates' policies than primordial issues and the water engulfing the capital has put flood prevention squarely in the spotlight ahead of the run-off election.

Both of the candidates claim vindication. Ahok said if he hadn't relocated people living on the riverbanks and widened rivers the flooding would have been far worse. He vowed to press ahead with his controversial policy, which has seen thousands evicted from their homes.

"When I came into office [as deputy governor in 2012] there were 2200 flood-prone areas. Last year, the number fell to 400," Ahok was quoted saying in The Jakarta Post.

He said that flooding in East Jakarta happened because the project to widen the Ciliwung River was only 40 per cent complete.

His opponent Anies Baswedan, who won the overwhelming majority of votes in polling booths near the demolished slum area of Bukit Duri, appealed to voters alienated by Ahok's policies when he called evictions an "injustice" during the election campaign.

Anies pointedly visited the inundated area of Cipinang Melayu earlier this week and said the floods were proof the incumbent's flood prevention program had been a failure.

"Anies so far has put in a big show of going to flood affected areas - I would be surprised if this isn't one of the examples he will cite in the next two months to criticise Ahok's policy," says Charlotte Setijadi, a visiting research fellow from the Yusof Ishak Institute in Singapore.

"But Ahok can spin it in his favour as well - he needs to keep doing what he has been doing for the last two years."

Setijadi said Anies had thus far been quite vague on his own flood mitigation plans other than to oppose Ahok's policies on forced evictions and the reclamation of Jakarta Bay.

"If he drums up this issue enough as attacks against Ahok, hopefully he does get pushed - particularly during the debate and by Ahok himself - to come up with an alternative solution."

A spokesman for Anies' campaign team, Anggawira, said Anies wanted to improve the city's sewage system and dams and improve river flows.

He also wanted to create water catchment areas in every house. "This is not a new program, the current government already started it, however it is not done massively," he said.

Asked about Anies' eviction policy, Anggawira said it was important to communicate with people who had lived on the riverbanks for a long time.

"We did not say we do not want to do evictions," he clarified. "If we said 'no eviction' we meant two-way communication, not a top-down approach with security apparatus to back it up. People want to have improved quality of life, they don't want to live in slums forever."

Kopral Suripto, 61, lives on the flood-prone banks of the Ciliwung River in Bukit Duri. Many from the area have already been relocated to low-rent apartments in Rawa Bebek in East Jakarta.

On February 16, the water was chest height in Suripto's home.

Asked if he would also like to be relocated, Suripto said: "Yes, why not? But the compensation should be appropriate.

"I think people who refused to be moved are not grateful enough because they were moved to a better place and the government provided free transportation for them to go to Bukit Duri. Actually, all people wanted to move but the compensation wasn't appropriate."