The development of a new port and associated infrastructure at Magogoni in Manda Bay near Lamu are among the major flagship proposals set out in Vision 2030. This is part of a long term vision to transform the economy of Northern Kenya by developing a Lamu Port and- Southern Sudan- Ethiopia Transport Corridor (LAPSSET) and it is, potentially, one of the largest infrastructure projects on the African continent. LAPSSET is set to include the port in Lamus Manda Bay; a standard-gauge railway line to Juba, South Sudan's capital; oil pipelines to South Sudan and Ethiopia; an oil refinery; three airports; and three resort locations in the Kenyan towns of Isiolo and Lamu and at the shores of Lake Turkana.
Lamu town is recognized by the Kenyan government as the oldest living town in Kenya. It is also a UNESCO World Heritage Site with a port that is said to be a thousand years old. Thus community resistance to the project is also motivated by concern is that the proposed port will destroy the history, heritage, and culture of the District.
The project will involve dredging shallow inland channels and felling shoreline-stabilizing mangrove forests. Experts say the process could disrupt artisanal fishing, the main source of income for around 70 percent of Lamu's 100,000 people, and destroy the environment, especially the mangrove plantations. In Lamu, the government has set aside 1,000 acres (404 ha) of land for the project. The Ministry of Lands says some 60,000 people may be displaced by the project. Furthermore in the Coast region less than 20 percent of residents have titles for the land they live on, making the land issue key. Many locals feel the port represents an additional 'land grab' by the government who is yet to institute land adjudication. They also complain of not being consulted and left out of the process.
Conservationists are also concerned that; construction of infrastructure will have an impact on River Tana, which is already facing challenges from existing and proposed developments. Water for domestic and industrial use will be drawn from river Tana, while the construction of the Lamu Port will stimulate major economic development opportunities and result in a massive increase in population which will exert further pressure on the resources in the Tana Delta.
By 2030, it is envisaged that the port and new town will be requiring 100,000m3/day and obtaining water from the High Grand Falls Dam, with an intake at the Nanighi Barrage (weir) and pumping a distance of 185 km, which has been considered as the prefered option among two other options.
In April 2013, Nature Kenya forwarded comments to NEMA on the project's EIA, rejecting it on grounds that the a Strategic Environmental Assessment ought to precede the EIA, making the project's EIA premature. This is because the project is a component of the larger LAPPSET project and therefore impacts need to be assessed holistically. Nature Kenya with funding from UKAid has been implementing a pilot program of Strategic Environmental Assessment and Land Use Planning in Tana Delta in order to address this and other conflicts in the region.
Feasibility studies for corridor components and the design of three berths and associated facilities in Lamu have been completed. The Kenyan government has set aside Kshs 2 billion for the construction of the three berth and a tendering process for the construction is ongoing.
The construction of Lamu Port headquarters is almost complete and the second phase of construction of the port which includes police lines and staff houses will be completed in June 2014.
A judge has allowed four human rights organisations to join a petition seeking to block the building of the multi-billion shilling Lamu port.
In June 2013, Four Human Rights NGOs opposing the project filed a court petition to stop the project. It has been referred to the Malindi High Court.