Runabouts, or other wake boats that use ballast water, will be confined to a stretch of the Waikato River as Biosecurity New Zealand clamps down on the freshwater gold clam.
The invasive pest clam was discovered in the Waikato River in April and could have been there for two to three years.
Biosecurity New Zealand director of readiness and response John Walsh said the Controlled Area Notice (CAN) affected boats used in Waikato River from the Whakamaru Dam south of Tokoroa, to the river mouth at Port Waikato.
Wake boat owners who used that area must not use their craft in any other waterways, including other parts of the Waikato River.
"Wake boats present a higher risk of transmitting the freshwater gold clam as there is currently no known reliable method of cleaning the internal tanks and bladders. Biosecurity New Zealand is investigating whether a reliable cleaning method can be developed. If so, the special requirements for wake boats will be reviewed."
Fish and Game New Zealand said it supported the CAN. Chief executive Corina Jordan said they have been asking for a 'ground zero' response.
"The high-risk transmission pathway has been closed down, therefore we should be less concerned about the transmission from Waikato to other areas."
She said other waterways were facing ongoing ad hoc closures as communities worried about the clam migrating via boats.
"Fish and Game recognise the concerns of our wider communities including anglers around the closure of Lake Ōkataina and potential wider closures of significant freshwater bodies in the Rotorua region and further afield," Jordan said.
"We are hoping the stronger focus on the Waikato River mean communities around the Rotorua lakes region are reassured that the right steps are being taken to reduce the risk of transmission to other valued lakes and rivers."
The CAN also meant all recreational river users in that stretch of the Waikato River would need to follow existing clam-specific 'Check, Clean, Dry' requirements for any craft, gear (such as fishing and other equipment used to gather kai) and equipment (including water skis, wakeboards and inflatable pool toys).
"Extensive surveillance shows that we are successfully stopping the spread of the clam," Walsh said.
"CANs are a critical tool in our ongoing efforts to protect our waterways. This new CAN replaces and strengthens the existing measures that are in place for the Waikato River and adds to the biosecurity rules we've put in place for Te Arawa lakes in the Bay of Plenty recently," says Walsh.
To support the clam-specific Check, Clean, Dry requirements of the CAN, Biosecurity New Zealand established a permanent wash station at Mighty River Domain, Lake Karāpiro. A mobile wash station was also being funded, which can be moved as needed to events and busy locations along the Waikato River.
Signs outlining the new CAN requirements are being installed along the river at about 70 different locations. These should all be in place by Sunday.