The Mekong River Commission (MRC) said in a statement released on Monday that another reason could also be because of the presence of algae at the river bottom.
The sections in Thailand's northeastern province of Nakhon Phanom and Laos' south-central town of Thakhek are now aquamarine, and the MRC said this could also be true of other parts of the river where low flows occur.
The river flows through China, Myanmar, Laos, Thailand, Cambodia, and Vietnam, and the region is experiencing one of its worst droughts ever.
The MRC has done a preliminary analysis of the causes and potential impacts of the phenomenon.
The fine sediments normally found in the fast flowing river and the great depth that give it its usual brownish color are conspicuously absent, making the water clearer.
This means that, when sunlight hits the river, the water absorbs what is known as the "long-wavelength colors" at the red end of the light spectrum and makes the river look blue. This occurs only if the water level is just a few meters.
The clearer water in turn allows microscopic plants and algae to grow on the sand and bottom causing the margins of the river to turn green.
The algae are normally flushed away by the currents, but this is not happening at Nakhon Phanom, and perhaps elsewhere, now due to the exceptionally low level.
The algae are in fact building up and this could be exacerbated if fertilizers used in agriculture enter the river and feed their growth.
"The blue-green water phenomenon is likely to spread to other stretches of the Mekong River where low flows are encountered," the MRC secretariat's chief environment management officer, So Nam, who led the study, said.
"The issues of low flows and sedimentation could possibly lead to adverse impacts that have been well quantified in the MRC Council Study."
Some of the potential impacts include a change in productivity of the river with less food becoming available to insects and small fishes, and reduced productivity of aquatic biodiversity, including fish, due to high water clarity.
This will in turn affect the fish catch and livelihoods of local communities.
High water clarity also leads to significant algal growth or algal bloom. This leads to high dissolved oxygen levels during the day, but very low levels at night, possibly affecting the lives of various fish species.
If the water clarity remains high, the algal bloom could cause thick green mats that rot and stink.
If the conditions worsen, the algae can change from green (Chlorophyceae) to blue green (Cyanophyceae), producing toxic substances that are harmful to animals.
But Nam said "it is unlikely such conditions will occur in the main river, and will be restricted to backwaters."
But he warned people to be careful about watering their animals if the water turns very green.
The present conditions might persist until flows increase with the onset of the next flood season in late May.
Conditions could also improve if large volumes of water are released from reservoirs in the Upper Mekong (Lancang) dams and tributary dams with the sediments that give the river its usual brown color.
The MRC’s monitoring of flows shows that dry season flows have increased in the past few years due to water release at reservoirs to produce electricity.