He said there was no one-size-fits-all approach to granting a consent of this nature, and that there must be "a holistic assessment of the impact", which took into account economic benefits as well impact to the environment.
Smith said the Act allowed for significant environmental harm if was to be remediated or mitigated to the extent it would be.
Justice Joe Williams raised concerns about the "great risk" of trading off material harm with economic benefits in a "chaotic ecosystem" such as this marine environment.
A Court of Appeal decision in April this year found that when granting the consent the decision-making committee for the Environment Protection Authority did not focus on its primary objective of protecting the environment, nor did it give explicit consideration to protecting the environment from pollution by discharges of harmful substances.
The Court of Appeal also found that Treaty of Waitangi principles were not adhered to, as tangata whenua have an existing interest in the marine environment and its resources as kaitiaki or guardians.
However, Paul Majurey, representing Trans-Tasman Resources, told the Supreme Court that the EEZ Act did not have a requirement for the Treaty principles to "be given effect to" and that decision-makers were only required to take them into account.
Legal counsel for iwi Ngāti Ruanui and Te Kāhui o Rauru and the environmental groups who are fighting the appeal made their case on Wednesday.
The civil appeal runs until Thursday.