Residents in the Lekki and Victoria Island suburbs woke up on Saturday morning to flooding in their homes and their cars submerged under water.
One brave resident took to swimming in the infested waters on Lekki road, an affluent suburb that is home to some of the most expensive real estate in the coastal city. A crocodile was spotted along Chevron Drive in the same neighborhood.
Another was spotted kayaking across Ahmadu Bello Way, Victoria Island, a usually bustling business district.
The past 40 years has transformed Lagos, infamous for its heavy traffic and poor air quality.
Nigeria's largest city and commercial capital has been hit by days of persistent heavy rain and storms at the height of the rainy season.
However, poor drainage systems and inadequate urban planning have compounded the effects of the downpour.
The state government issued a statement urging residents in affected areas to stay at home and for those living in lowlands to 'move uplands.'
"You are implored as much as possible to stay indoors unless it is essential to your safety and livelihood," said Samuel Adejare, the city's environment commissioner.
He added: "We are on top of the situation.. our emergency lines 112 and 767 are open for residents to report any emergency situation."
Lagos is one of the fastest growing cities in the world and a 2008 report warned that millions of people were at risk of losing their homes because of rising sea levels.
"Lagos is a megacity with 15 million people, half of them at two meters (6 ft) above sea level, and that puts them at risk as hardly any other big city in the world," Stefan Cramer, Nigeria director of Germany's Heinrich Boll Foundation think-tank and an adviser to the Nigerian government on climate change, said at the time in a Reuters news report.
The city was recently admitted to a 100 Resilient Cities
program by the Rockefeller Foundation to fund a chief resilience officer for African cities.
"Africa is one of the front lines in terms of urbanization globally. People are moving out of the villages and into the cities at a pace unprecedented in history," says Michael Berkowitz, President, 100RC.
The aim is to provide a model for what a new, more resilient urbanization might look like.
"It's one of the biggest cities in the world, and therefore incredibly complex," Berkowitz says.
Nigeria's population of 187 million is expected to double by 2050
, making it the fourth most populous country in the world — with the world population predicted
to hit the 10 billion mark in 2053.