The construction process for the Port of Miami Tunnel was always going to be challenging, as the MacArthur Causeway Bridge (to which the tunnel was due to connect) could not be shut down, and the port itself also needed to remain in full operation. The tunnels were the first tunnels in Florida to be completed using a tunnel boring machine (TBM), which has substantial upfront costs.

The first tunnel took eight months to complete, which was longer than originally planned, due to unforeseen geotechnical challenges. A large amount of coral stone, a hard material similar to granite, slowed down the boring from the start. However, more significantly, 30 metres below sea level the construction contractor encountered voids filled with a semi-liquid slurry which, in some locations, were the size of a city block. It was not possible to bypass the voids, nor leave them filled with the slurry. The solution to this challenge was to pump approximately 200,000 cubic metres of concrete into the voids, allowing the TBM to tunnel through a stable material. A contingency fund had been put aside by the Procuring Authority and the Project Company to cover additional costs due to geotechnical issues, and this was used to pay for this extra work. However, agreeing to reimburse the Project Company in recognition of the additional costs led to a dispute. This is described in further detail under the heading "Key Events" below. There were multiple work-fronts open at the same time, so the construction contractor was able to reschedule and optimise its work and mitigate the delays caused by the challenging ground conditions.

A final tunnelling challenge to be addressed was the existence of groundwater, which threatened to disrupt the construction of cross passages between the two main tunnels. To avoid water pouring into the space that was being dug out, the construction contractor had to freeze the area to -30 degrees Celsius and keep it cold for 40 days to give the salty water time to harden.

Regardless of the challenges faced during construction, effective management of the construction phase and collaboration between the key parties resulted in completion of the project ahead of schedule and under budget.

The construction contractor also faced some challenges in terms of having a full understanding of and compliance with federal laws and regulations, particularly labour laws. It is very important that the Procuring Authority ensures that the Project Company and its contractors are fully aware of the federal laws affecting the works. Regardless of the risk allocation, serious violations of labour or safety laws will have a negative impact on the project and all parties involved from a reputation point of view. The Procuring Authority was also liable for fines if any of its projects were not compliant with relevant laws and regulation. In this project, the construction contractor hired a labour union company to assist it in complying with the federal labour laws.