The 120 km SGR phase 2A line between Nairobi and Naivasha is being constructed at a cost of Sh150 billion (about 1.5 billion USD) financed by the Exim Bank of China and the Government of Kenya. The Stretch between Mombasa and Nairobi was the first part of the two-phase project. Phase 2B of the project will run between Nairobi, Naivasha, Narok, Bomet, Nyamira and Kisumu. It will also include the development of a new high capacity port at Lake Victoria, Kisumu. Phase 2C of the SGR will connect Kisumu and Malaba through Yala and Mumias.
Kenya Railways had said that the original route would require taking over multiple acres of residential and industrial land, which will cost it huge sums in compensation payments. These include parcels owned by Bamburi Cement, Devki Steel Mills, Athi River Steel Plant, Kapa Oil Refineries, Orbit Chemicals, Muthama Heights Estate, Kenya Meat Commission, ISL Kenya and Murumbi African Heritage House, among others.
Several park-based options were also considered initially, including one that would have cut through a rhino-breeding zone, before the authorities settled on raising the track onto a bridge with underpasses so that animals could move around the rail line. Already, 216 acres of park land have been dedicated to 12 kilometers of railway. This decision has conservationists and nature lovers up in arms over the long-term integrity of this ecosystem.
On 13th September 2016, Kenya Railways Corporation (KR) and the Kenya Wildlife Service (KWS) announced that they plan to build the second phase of the standard gauge railway (SGR) right through the middle of Nairobi National Park (NNP).  Friday, September 16th, 2016. Dozens of angry people have marched in the Kenyan capital Nairobi to protest plans to build a railway line over the Nairobi National Park. The protesters included conservationists and others who wore T-shirts and carried banners saying "don't rape our park."
The proposed railway alignment shows the new design that curves deep into the Park for about 50km before exiting near the Kenya Wildlife Service main gate on Langata road. In July Kenya Wildlife Service agreed that the SGR could route through around 250 acres of the Nairobi National Park near Mlolongo to protect Alan Donovan's African Heritage House. But this new proposal makes vastly greater inroads and will compromise almost 20 percent of the park. Thousands of residents and the steadfast environmentalists officially delivered an open letter to President Kenyatta and copied it also to KWS, arguing that protecting the country’s rich natural heritage from environmentally destructive development is the government’s responsibility. 
The National Environment Tribunal issued a stop order, after it was realised that the route was finalised without conducting an Environmental Impact Assessment (EIA), which is a compulsory requirement for all development projects. The stop order specifically prohibits any ‘activities’ related to SGR Phase 2A from being conducted until the matter is heard and determined in court. On 4th October, the High Court in Nairobi upheld the petition of conservation groups to stop work on the planned route through the park which by common consensus is to avoid irreversible damage to the ecosystem. However, on 20th October, the construction of the phase-2A began in spite of this order.
On Saturday 29th October, 2016, more than 400 people gathered to object to the government’s decision to route phase-2A of the Standard Gauge Railway (SGR) project through the middle of the Nairobi National Park. The organisers urged the relevant authorities to begin open and transparent dialogue between key stakeholders to try and find a responsible and lawful solution, as this high-profile development case could set a precedent for how the country manages its natural resources in future.
Nairobi National Park then became the focal point of a conflict between national development priorities and environmental conservation in Kenya. Established in 1946, this 117-square-kilometer wilderness area is the oldest state park in Kenya, and home to incredible biodiversity. Animals such as buffalo, giraffe, lions, leopard, white rhino, the endangered black rhino, and more than 600 bird species live inside the protected area, which is also the only national park in the world within a city. "We are really perturbed. We are setting a precedent that spells doom to our parks. If this trend is not stopped, in the next 20 years our parks will be replaced by infrastructure projects and commercial development. We will say goodbye to our wildlife and other ecological zones", said by protesters.
There was no clear explanation why Phase 2 of the SGR will no longer follow the route of the Uganda railway, presently operated by RVR, as originally proposed. However, it’s reported that some government officials believe that Nairobi National Park is a waste of land and running the railway inside the park would be more economic than purchasing private land or reclaiming grabbed land next to the old railway. “As we speak, all approvals have been done without public involvement or following due process," the source said to the Nairobi daily newspaper, the Star.
The train isn’t the only threat to Nairobi Park, which is under pressure on several fronts. The population of Nairobi has burgeoned from 2 million people in 2000 to over 3 million at present, and residential and commercial districts surround the northern, eastern, and western borders of the park. Trash and effluence in rivers flowing through the park is of concern. An oil pipeline runs below the park, and pylons of electricity lines stretch from north to south.
In 2011, a section of land was hived off the park to build part of a large motorway. The southern park boundary, historically left unfenced to enable the seasonal movement of animals, is constantly under threat from encroachment and land development, which, if not controlled, could turn the park into more of an oversized zoo. The question remains whether this small and delicate ecosystem can sustain any more infrastructures.
Environmentalists are not convinced by an environmental impact assessment report for SGR, not least because it was carried out after railway construction had commenced. They argue that the process was rushed, that there was insufficient stakeholder engagement, and that the assessment was short on many specifics. Railway work inside the park is expected to take 18 months, but it remains unclear what effect noise pollution, building works, and escalated human traffic will have on the habitat and wildlife behavior in the short and long term. On October 27, 2016 WildlifeDirect convened a forum bringing together stakeholders from many sectors, who were unanimous in calling on Kenya Railways to search for an alternative solution that would preserve the integrity of the Park. However, on December 13th, 2016, NEMA issued a license giving Kenya Railways the go-ahead to construct SGR Phase 2A that will pass through the middle of Nairobi National Park on an elevated bridge. Those efforts have fallen on deaf ears and the Park now faces an uncertain future.
In addition to impacts on wildlife, the train could also impact tourism. Nairobi National Park attracts the third highest number of visitors in Kenya and is one of the few green spaces for city residents. Tourism is the second highest source of foreign exchange in Kenya and KWS primarily generates its income from park entry fees. The park also provides valuable ecosystem services of purifying the air in Nairobi and serving as a watershed. Insects and birds from the park are pollinators in peri-urban farms, hence playing a vital role in food production.
Given the many impacts of the train, environmental advocates have taken their battle to court. In April 2017, Kenyan activist Okiya Omtatah and the Kenya Coalition for Wildlife Conservation obtained a court order to suspend construction works inside the park on the basis that the environmental impact assessment was insufficient. The case is still being heard. Kenyan conservationists claim that they are not against infrastructure projects but question the government’s commitment to sustainable development and public participation as enshrined in the Constitution. And they worry about the precedent the SGR project may set when it comes to other mega projects in or near Kenya’s national parks.
The decision to route the railway through the Park not only goes against public opinion, but it also ignores the advice of numerous scientific experts who have warned of its irreversible consequences. Moreover it sets a very dangerous precedent for other Protected Areas in Kenya threatened by infrastructure projects, mining, and unregulated urban and agricultural expansion. It especially undermines the budding conservancy movement in which hundreds of Kenyans have invested their land in conservation.
Although it was reported that the work on Phase 2A would resume from September 2017, later it revealed that the increased land disputes in parts of Mai Mahiu in Naivasha are delaying the extension of the SGR from Nairobi to Olkaria.