The Cyanobacteria blooms were more common at this time of year, with really warm temperatures, long daylight hours, and low flows in rivers - which had exposed the bacteria "mats" in sections of the Tukituki River.
As some parts of the bacteria are toxic to humans, and animals, she said people should swim somewhere elsewhere until it washed away after heavy rainfall.
In response to water sample results at Maraetotara Lagoon showing E. coli levels four times above safe swimming guidelines, a digger had removed a barrier so there was an outflow from the lagoon to the sea.
If there was another E. coli exceedance in next week's testing the council would track where the faecal matter had come from, she said.
Overall, this summer "hadn't been too bad" for water-quality issues, Ms Madarasz-Smith said.
"Each summer is so different, it's very climate driven. We find when we have a lot of rainfall we can get exceedences, exceedences, exceedences."
Bursts of sudden heavy rain after dry periods - which have marked this summer - could have an impact on water quality as they could wash things into recreational waterways.
Monitoring means the scientists can also take proactive steps if they find higher levels of E. coli by tracking the faecal matter to its source, and stopping this from entering the waterways.
She said it helped that people were a lot more aware now of the causes, and issues around water quality.
There had been a big uptake in the council's updated swim safe tool, which was re-released early this summer. It allows people to check the condition of certain waterways, which are marked with green (safe), amber, or red (don't swim) dots.
"Traffic's up 350 per cent on this time last year. It's been a really great module to work on because we're working to give people better information, and we're working to actually try to change what they do," Ms Madarasz-Smith said.
Although the tool made it easy to see which waterways were okay, she urged people to still consider the conditions before swimming - whether there had been recent rain, the surrounding environment, and how clear the water appeared.
-To check if it's safe to swim check "Can I swim here" at lawa.org.nz