Waterways are very vulnerable to weeds, especially if the riparian area has been cleared.  They destabilise the banks by outcompeting natives, causing erosion. They will also act as vectors (distributors) of the weeds, spreading them to areas downstream.

Pond Apple (Annona glabra) was introduced as a root-stock for orchard trees and some dense and extensive invasions of have established in lowland areas south of Noah Creek and disturbed areas along the Daintree River. Pond Apple has the potential to destroy the Melaleuca communities by invading the understorey and blocking their regeneration.   

Hymenachne, a pasture grass, and Nabua sedge are also a problem in the Daintree.

Outdoor ponds are going to overflow during the wet season and anything in them (including fish) will make their way to the waterways - use indigenous plants and fish.