The initial EIA process began during the planning phase of the project from 2001 to 2003. As a result of various route re-alignments and design changes proposed by the Project Company, the EIA process had to be updated during the construction phase and was completed in 2009.

The protracted EIA process spanned eight years and had two major implications: the costs associated with the EIA process were much higher than originally anticipated and EIA consultants appointed by the Project Company left the project during the lengthy process, which led to a lack of knowledge continuity.

The timing of the EIA process posed a challenge, as detailed above under the sub-heading "Construction Phase". The EIA regulation at the time did not provide for a seamless transfer of environmental compliance responsibility from the initial applicant (i.e. the Gauteng Department of Public Transport, Roads and Works) to the Project Company. This contributed to disputes between the Project Company and the Procuring Authority.

As a result of the requirement for the implementation of the EIA process by the Procuring Authority before the contract award and final design development, much of the process had to be redone by the Project Company to address changes to the route alignment and final design development completed. The risk for the detailed EIA is commonly transferred to the Project Company at the contract award.

There have been disagreements between the Procuring Authority and Project Company related to the responsibility for compliance with the conditions attached to the authorisation to proceed with the project, as part of the EIA process. This resulted in a dispute that was resolved in arbitration.

There have also been disputes between the Gauteng Department of Public Transport, Roads and Works (as the project proponent and applicant for EIA authorisations) and some public participants in relation to the route alignment of the project, following the comprehensive public consultation process. Most of the disputes were solved by the Gauteng Department of Public Transport, Roads and Works accepting and implementing the proposals made by residents for alternative route alignments, but some disputes led to litigation which resulted in a decision in favour of the Procuring Authority.