The log yard, owned by Eastland Port, has been closed since the middle of 2016.
The company applied for resource consent to develop the log yard and upgrade the wastewater system last year. A decision on the consent is yet to be reached.
General manager Andrew Gaddum said as the log yard was not in use, it was unlikely to have been the reason there was any discolouration in the inner harbour.
“Excess stormwater . . . can often lead to changes in the harbour’s water colour.
“There are multiple influences that contribute to stormwater discolouration in the inner harbour during heavy rain with a 200 hectare catchment.”
In 2015, the port installed a “world-class” water treatment system in its upper log yard to clarify water leaving the area.
Port contractors carried out routine water sampling as part of the port’s stormwater discharge consent conditions last week.
The results will be known by the end of the month.
Gisborne District Council said it was investigating the discharge, whether it came from the log yard and whether it breached any of Eastland Port’s consents.