Lake Tanganyika is Africa's deepest lake and is getting deeper, swallowing entire neighbourhoods along its shores at Burundian capital, Bujumbura.
According to experts, climate change and deforestation in the highlands and water catchment areas are causing topsoil erosion and an increase in silt in the lakes.
Experts say if both trends are not reversed, the lake will continue to rise, creating climate refugees in the process.
Thomson Irakoze navigates his boat through the flooded streets of his neighbourhood in Burundian capital Bujumbura, now submerged by the rising waters of Lake Tanganyika.
"After the neighbourhood was flooded, the residents fled to places that were still dry to try and build small slums" he explains.
Hundreds of families are under threat, as water levels along the shores of East Africa's great lakes continuously increase.
Surging waters have caused the displacement of people living near the lakes.
In Bujumbura, submerged homes, schools, and businesses are forcing families to move to higher ground.
The water has been rising steadily over the past ten years, but in the last year, it has gone up by more than two meters, according to some residents here.
Locals are living in makeshift tents, hoping nature will have mercy on them and waters will eventually retreat to their original levels.
"After the waters rose here in Mushasha and our homes were flooded, we have had to go to higher ground to try and rebuild our homes," says resident Violet Irakoze.
Her neighbour, Jean Marie Barwiza, adds:
"We trust God who can help us. We will wait for the level of the lake to come down again or for the state to offer us another place to build, we would be grateful."
Scientists say heavy rains in East Africa made 2019 one of the region's wettest years on record, the water drained into lakes, causing flooding.
Elias Niyongabo, works for the Burundi Government Ministry for the Protection of the Environment:
"As we are in a context of global warming of the oceans, it is very likely that the humidity of the planet in general will increase," he says.
Burundi experienced heavy rainfall this spring, according to the Geographic Institute of Burundi, washing sediment into lakes.
"There are abnormally high movements of sediment that then settle. So, if there is sediment in the water, it obviously occupies the volume that would normally be occupied by water, so the water level rises," explains Niyongabo.
Rising lakes are not just affecting Burundi but appear to be rising elsewhere in East Africa.
Dr. Richard Mwita, assistant director of Kenya's Meteorological Department says there are three theories:
"The very first one has to do with the global or general weather circulation patterns caused by the rising levels of the sea surface temperatures in the Pacific Ocean as well as Indian Ocean and other global oceans. They cause a rise in rainfall, and this increases the water levels they reach the lakes," he says.
"The second one, is largely geographical geological, where the researchers say that there are tectonic shifts within the earth surface, and this tends to shift the ground water which tends to cause a rise in the lakes.
"Then the third one is basically about deforestation and sedimentation. So, after the land is deforested to pave way for agriculture and other activities, you have a lot of sediments which get their way into the lakes and hence they reduce the depth of the lakes and therefore the water rises."
"In Lake Tanganyika, reports are that the lake rises have been reported around 2020. This was between 793 meters to slightly above that and this is something that had not been witnessed since 2013 and it was largely attributed to the rising rainfall amounts within that region," he adds.
The United Nations' International Organization for Migration says more than 52,000 people have been affected by flooding since March this year in Burundi, though that figure is likely to be an underestimate.
IOM data says there were 127,775 internally displaced persons in the country as of May 2021, mostly due to natural disasters.
In Kenya, lakes have also been steadily rising over the past ten years, submerging towns, displacing residents, and threatening wildlife with extinction.
The Rift Valley region has always been unstable geologically, its name refers to a fracturing of the Earth's crust, where two tectonic plates collide.
But now, deforestation in the highlands has decreased the permeability of the soil, recent heavy rainfall has swamped much of the low-lying land.
Without forests, the rain erodes the land, washing tons and tons of silt into lakes.
This clogs underground drainage fault lines which means water cannot drain out of lakes, causing water levels to rise dramatically, following the 2019 rainfall.
The lakes rise cyclically every 50 to 60 years, what is new is the intense rainfall and rising temperatures.
Mwita says good planning by authorities will help manage the crisis.
"The future would likely be that if there are no mitigation measures put in place, we are likely to see more damages to people due to the rises. Particularly the displacement of people and also property. However, if proper mitigation is put in place, we are likely to be able to manage this rises," he says.
"The global solution is largely mitigation which is highly linked to trying to manage climate change from the Paris agreement, if we can retain the global average temperatures to below 1.5 degrees Celsius within the next ten or so years then that would be a really good action towards limiting the impact of lake level rises and other impacts of climate change."
Glasgow, Scotland's largest city, will host the delayed U.N. COP26 climate summit later this year.
It's been billed as a "last hope" to keep emission-cutting commitments made in the 2015 Paris climate accord.
The commitments made by global leaders there may affect the long-term future of people living along the shores of East Africa's Great Lakes region.