"We will be doing ongoing testing and monitoring over the summer," Mr Hughes said.
"We just have to wait for the bloom to go away."
Meanwhile, Horizons Regional Council is still monitoring Dudding Lake and Lake Wiritoa.
Horizons water quality expert Barry Gilliland said algae counts had fallen at Dudding Lake and were within acceptable guidelines.
Algae counts were still high at Lake Wiritoa but this algae was not toxic, he said.
"The usual advice [is] to mix the surface water up by doing a few circuits of the lake in a power boat before undertaking activities like water skiing. Although no surface scums were observed when sampling, this is simply a precaution to mix any algae into more of the lake water if it is concentrated near the surface, especially first thing in the morning," Mr Gilliland said.
He said blue-green algae thrived in warm temperatures and stable water conditions.
Four of the six swimming spots Horizons tested for water safety had come back clear in the latest round of testing. They are Kai Iwi and Castlecliff beaches, Mowhanau Stream and Whanganui River at the city bridge. The water at Lake Wiritoa and Dudding Lake was acceptable.