He said if that happened, the algae were likely to "bloom and die" quickly, within just a couple of weeks.
Mr Gilliland said blue-green algae thrived in warm temperatures and stable water conditions.
"That is certainly the case at both these lakes. In the shallow water the temperature is around 22C and the algae are responding to that."
Testing had been done in the Whanganui River at the City Bridge but it was clear, he said.
"The rivers and streams in the Wanganui district are not suited to blue-green algal growths," Mr Gilliland said.
Public health protection officer Bruce Butters said he was keeping a watching brief on algae levels.
"The levels are certainly creeping up, and we are watching cautiously," Mr Butters said.
Mr Butters said of most concern was Lake Wiritoa, because it was such a popular lake, used for a wide variety of activities.
Blue-green algal blooms are affecting waterways throughout the country. Lake Okaro (Bay of Plenty) and Rotokauri Reserve (Waikato) were closed last month, Tomahawk Lagoon (Otago) was closed earlier this month, and warnings have been issued for the Hutt River.
Mr Gilliland said the settled weather had meant very clear test results for Castlecliff and Kai Iwi beaches, although the beaches were tested for E coli, not algae.
He said Castlecliff was the most consistently clean beach in the entire Horizons district, although he warned that no beach was safe for swimming for several days after a flood.