A beach in Wellington and a stream near Dunedin have been closed by pollutants and authorities are warning people to stay out and keep their animals out of the water.
Owhiro Bay in Wellington has been closed since Friday and will remain closed until at least Wednesday.
Blocked sewer pipes are believed to have contributed to the high levels of contamination found in the water there.
The Silver Stream in Mosgiel, south of Dunedin, is also closed to swimming after the discovery of a toxic algae in the area.
Two dogs died after ingesting the shiny, black algae which attaches itself to rock or in stream weeds.
Dried algae on the stream edges can also be toxic.