The area near the berth was being used to load logs on to a ship and he saw log debris around.
The officer had a sample of the stormwater analysed and found it contained 1200 grams of "suspended solids concentration" per cubic metre.
To be allowed under the council's environment plan the concentration had to be under 150 grams per cubic metre, except during a 10-plus year storm.
The council said the rainfall did not reach that level.
The port did not have resource consent to discharge "contaminated" water from the berth into the harbour, which made it an offence against the Resource Management Act.
The notice ordered the port to cease the discharge and submit to future compliance inspections.
The port has 15 days to lodge its appeal against the August 24 notice.
The Port of Tauranga recently revealed a profit of $94.3 million last financial year, off the back of record annual earnings and cargo volume increases.