At least 11 people have died in the operation since March 2016
Human rights group Amnesty is calling on authorities in Nigeria to stop "a violent, unlawful campaign" of demolitions and forced evictions in Lagos State.
It claims more than 30,000 people have been forcibly evicted from settlements in defiance of court orders.
Amnesty says the evictions of waterfront communities have so far left 11 people dead.
A new report, The Human Cost of a Megacity: Forced Evictions of the Urban Poor in Lagos, details repeated forced evictions of the Otodo-Gbame and Ilubirin communities carried out since March 2016 "without any consultation, adequate notice, compensation or alternative housing being offered" to those affected.
It also says some evictees drowned as they fled police gunfire, while at least one was shot dead.
Colm O'Gorman, executive director of Amnesty International Ireland, says: "These ruthless forced evictions are just the most recent examples of a practice that has been going on in Nigeria for over a decade in complete defiance of international law.
"For the residents of these deprived communities, many of whom rely on their daily fish catch to make a living, the waterfront represents home, work and survival.
"Forced evictions mean they lose everything - their livelihoods, their possessions and in some cases their lives.
"The Lagos state authorities must halt these attacks on poor communities who are being punished for the state’s urban planning failures."
Amnesty International says it spoke to 97 evicted people as part of its research.
It says in the first eviction, at midnight on November 9th, police and unidentified armed men chased out residents with gunfire and tear gas.
It also says homes were set on fire as bulldozers demolished them.
Evictee Celestine Ahinsu told Amnesty International: "After a couple of days we started seeing the bodies floating. I saw three - a man with a backpack and a pregnant woman with a baby on her back.
"The community youths brought the bodies from the water. The relatives of the pregnant woman and child came to take their bodies."
Nine people are believed to have drowned during the eviction and another 15 remain unaccounted for.
Amnesty says of the 4,700 residents who remained in Otodo-Gbame after the eviction, some slept in canoes or out in the open, covering themselves with plastic sheets when it rained.
Four months later, in March 2017, state security forces backed up by unidentified men armed with machetes, guns and axes forcibly evicted those who had remained.
It says when residents protested, they came under attack from police.
Meanwhile, 823 residents of the nearby Ilubirin community were forcibly evicted between March 19th 2016 and April 22nd 2017.
Amnesty says they were given just 12 days’ written notice of eviction.
It says Lagos state government officials and dozens of police officers chased residents out of their homes, and demolished all the structures in the community using fire and wood cutting tools.
Evictees subsequently returned to the area and rebuilt their structures, but these were demolished six months later with just two days’ oral notice and no consultation.
In November 2016, the Lagos government denied any responsibility for the forced evictions and blamed them on a communal clash that resulted in fires which razed down the community.
In March 2017, the government said its actions that month were taken to protect environmental health.