Polluted tributaries draining into Thwake dam will be cleaned following orders by President Uhuru Kenyatta.
The President spoke while inspecting the project in Makueni last Friday.
Authorities are putting clean-up strategies in place.
The President Nema to start cleaning the Nairobi River, which contains heavy metals, and other rivers upstream to ensure water fed into the dam is safe for human consumption
“We are going to ensure there is no pollution upstream because every Kenyan has a right to clean water,” President Kenyatta said.
His order came days after Auditor General Nancy Gathungu raised alarm about the safety of the water that will be fed into the dam.
The auditor said the Sh82 billion Thwake dam may turn out to be a white elephant because of polluted, unsafe water.
An environmental and social impact assessment of the project warned that the water would be hard to treat owing to the pollutants.
It cites problems of residual faecal and organic matter from pit latrines, graveyards and waste holding sites from displaced homesteads and social locations.
The situation undermine the health of people and animals drinking he water.
Gathungu said the Water ministry has not taken corrective measures to ensure the water is safe.
She said the dam’s main supply will be the Athi River whose main tributary is the Nairobi River polluted with heavy metals.
About two million people from Lower Eastern are planning to use the dam to end their water shortage.
The dam, which is being constructed downstream from Thwake and Athi River, covers 2,470 acrs (10 square kilometres) to create a reservoir of more than 690 million cubic metres.
On Wednesday, at the Michuki Memorial park, the ministries of Environment and Forestry, Water, NMS and Nema set out strategies on how to carry out the clean-up.
Water CS Sicily Kariuki, NMS director general Mohammed Badi, Nema DG Mamo Mamo, UN-Habitat executive director Maimunah Sharif and Kenya Forest Service chief conservator Julius Kamau were present.
NMS and UN-Habitat signed an MoU to enhance cooperation and promote communities' role in improving their city.
Kariuki said river pollution must be controlled to reduce health problems.
The CS said the Sh1.29 billion in investments in sewer lines yielded results. The rollout is expected soon and will improve sanitation.
Sharif said UN-Habitat will help the government improve green spaces and urged authorities to provide non-motorised transport.
Nema DG Mamo said the urban rivers regeneration programme is being implemented over five years.
The programme is in the second year and has prioritised the Nairobi Rivers due to the high levels of pollution and depletion of riverine ecosystems.
The Nairobi River is the main source tributary of the Athi-Galana-Sabaki River, which is the second-largest river within the larger part of South Eastern and Coastal areas.
The DG said 70 per cent of pollution points are in sections of the river upstream of the CBD and Michuki Memorial Park.
The river quality has improved from its "awful" state earlier, he said.
The upstream section comprises the main Nairobi River tributary, also known as Nyong’ara River that originates from the Ondiri swamp in Kikuyu area.Other tributaries are Kirichwa Kubwa and Kirichwa Ndogo.
Mamo said the same activities have started along Ngong River and Mathare River which are downstream of the CBD and are highly polluted and depleted.
The DG said informal settlements contribute to a much of the pollution and are the greatest obstacle to improving water quality.
Mamo said restoration and stabilisation of river banks and floodplains were on course.
“Beaconing and rehabilitation of the riparian zones should then immediately follow and start within Kirichwa Kubwa River along with the Nairobi Arboretum,” he said.
However, adequate resources are lacking.
NMS director general said the city’s rivers are noxious chemical concentrations of raw human, industrial and medical waste. They damage the environment and the quality of both surface and groundwater.
They kill aquatic life and increase disease.
“The resulting environmental degradation and public health impacts lead to high child mortality and morbidity, poor school attendance and performance, especially for the girl child, and low productivity,” NMS boss Badi said.
Edited by Kiilu Damaris