Peter Leweri the naturalist at the plush Island Camp Resort Baringo, which sits on Lake Baringo’s Ol Kokwa Island in Kenya’s Rift Valley, pulls out a fish and flings it high into the air.

The tilapia lands with a plop on the lake’s jade-blue water, but the African Fish Eagle perched on a nearby rock ignores it.

It’s unusual for the fish-eating bird to ignore a free meal. But there is good reason it has done just that in the recent past. The lake is full of fish and is almost overflowing, that even Ol Kokwa Island is separated into three for the first time in living memory.

Until 2010, the water levels of Lakes Baringo and Bogoria, which lie about 25 kilometres apart, were so low that many predicted they would soon dry up. Now both lakes are twice their “normal size,” with a possibility that they could merge, creating one big mass of water.

This presents some scenarios. If Bogoria, the alkaline lake, flows into the freshwater Lake Baringo, the latter could turn slightly alkaline attracting more flamingoes. And if Baringo, the freshwater lake flows into Bogoria, the flamingoes could desert Bogoria – but nobody knows for sure.

William Kimosop, born in Baringo, and is the chief county warden said that he first noticed the lake levels rising in September 2012.

“It was a very unusual rise that even the wazees (old men) had never seen. Then during the drought of January last year, the water did not recede,” said Kimosop.

The rains increased by the end of 2013, and water levels in both lakes rose further. Lake Bogoria’s present size is 70 square kilometres, while Baringo’s is approximately 300 square kilometres compared with its average size of 168 square kilometres.

“Height-wise, Lake Baringo is lower than Bogoria,” said Kimosop. “At present, they are almost at the same level. Any further rise — like 10 feet this year — will mean Bogoria flowing into Baringo.”

The water submerged all roads in the Bogoria National Reserve forcing a new network to be built on higher ground – more than once. The ring road around Lake Baringo was submerged too. Homesteads, schools and livestock grazing fields are under water too, forcing area residents and heir livestock to move to higher ground. The famous hot water springs on both islands are submerged including the smaller islands on Baringo like Rongena.

The Lake Baringo Club, once a luxury holiday resort is completely under water as is the snake park. The popular Roberts Camp too, has moved to higher ground.

“Human-wildlife conflict has also increased,” said Kimasop. “There are more incidents of crocodile and hippo attacks on people.”

“It’s not good if the lake rises,” said Salina Lekangurura said to be the first Njemps woman to start fishing on the local kadich (canoe) in the deep waters of Baringo in 2010.

“It has destroyed our houses and trees. I have had to move to higher ground and I am now living in a tent donated by the Kenya Red Cross. But on the other hand, the fishing is good.”

There’s documentation of both lakes rising between 1961 and 1964 by 2.5 metres. At that time, Betty Roberts’ house (founder of Roberts Camp) was submerged up to the first floor. The lakes’ waters then subsided, only to rise again now — a span of 50 years, with the water levels decreasing in a span of about five years.

The rise and fall of the lakes of the Great Rift Valley, the Albertine Rift and others is not new to science. Lake Victoria, Africa’s largest lake and the world’s second largest freshwater lake sitting in a depression between the East African Rift Valley and the Albertine Rift (western arm of the East African Rift system) has dried up at least three times since its formation some 400,000 years ago. Twelve thousand years ago, it was a desert.

Lake Turkana in Kenya’s Great Rift Valley almost dried up in 1900 and 1939 yet in 1888 it was a large water mass.

“In a paper co-authored with other Kenyan scientists titled Geospatial Extent of 2011-2013 Flooding from the Eastern African Rift Valley Lakes in Kenya and its Implication on the Ecosystems, Simon Onywere, a professor at Kenyatta University in Kenya, writes that the recent rise in all Rift Valley lakes correlates to a longer residence of the Congo Air Mass in the Western Highlands of the Rift Valley, bringing in longer periods of rainfall.”

But perhaps the bigger question is: What drives the sudden explosion of heavy rainfall that causes the water levels of lakes of the Great Rift Valley and others to rise so phenomenally?

Dr Bonnie Dunbar the director of Island Camp Resort Baringo and managing director of Omega Farms, in her research came across a paper published by Dr Norman L Miller in the Climate Science Department at the University of California, Berkeley in the US. Miller predicts that with the polar ice-caps melting, the moisture at the Equator increases resulting in more rainfall.

The effect of the Polar ice-caps melting has far-reaching consequences such as the glaciers on Mount Kilimanjaro completely melting away by 2020.

“The bottom line is that nobody knows what’s happening,” said Dunbar. “If there was more money invested in research on lakes and climates, we could determine for example what kind of dams to build or fish numbers to stock. Without research, it’s difficult to make informed choices.”

Perry Hennessy, co-director of Island Camp Resort Baringo makes an interesting observation.

“Fifteen kilometres north of Loruk which is the top end of Baringo, the lake drains into the Turkana basin. The water passes under the road and there is a place where it flows out. In the 1920s, an Indian dug a borehole but all he got was hot water so he capped it,” he said. “The concrete is now broken and you can watch the lake (Baringo) water go straight down. So why not open the hole and allow for the lake water to flow into River Tana and eventually into Lake Turkana? It’s a desert place that could do with water. But nobody is bothering to find out.”

In any case, for now the increased water levels in the two lakes are an exciting phenomena to watch — and whether they will merge is anybody’s guess.