Swimmers at Stephens Bay Lagoon in Tasman are risking their health, with faecal bacteria present more than half the time in the water.
Concerns have also been raised about the nearby Kaiteriteri Beach and a stormwater pipe, found with disease-causing organisms, which "is like a magnet for children".
Sampling of swimming sites around Tasman during the 2023-24 season found that the proportion of the bacteria at the Stephens Bay Lagoon exceeded alarm guidance 54 percent of the time.
This far exceeds second place Rototai at 20 percent and third's Port Riuwaka at the mouth of the Riuwaka River at 17 percent.
However, Stephens Bay Beach - outside of the lagoon - has good water quality which did not exceed the alarm level at all, and only exceeded the alert level once, over the season.
Tasman District councillor Trindi Walker was "quite concerned" by the levels of faecal bacteria because the lagoon was a considered a safe place for children to play.
She asked what the council was doing to raise awareness about the issue, particularly for people who did not live nearby.
"We have a groundswell of people who don't actually live locally who come and utilise that area."
Trevor James, a senior freshwater and estuary scientist at the council, said warning signs were in place and that the council frequently communicated the risk levels at the lagoon during the swimming season.
Faecal bacteria has been a problem at Stephens Bay for several years.
In January, "very very high" levels of enterococci and faecal bacteria were detected at the lagoon prompting calls for swimmers to avoid the area because the number of bacteria could cause illness.
And earlier in March 2022, a fatberg caused a raw sewerage overflow into the Stephens Bay wetland which then drained into the ocean.
However, a hole drilled through a lateral sewer pipe might have been causing trouble in the area for about six years, even prior to the 2022 overflow.
James told councillors that it was possible that bacteria from the 2022 overflow had remained and became naturalised and were now growing in the wetland, impacting samples from the lagoon.
"That is perhaps the thing that is causing this to last longer than perhaps we would have expected."
However, the council continues to undertake extensive investigations in the catchment and around the area to look for other potential sewerage leaks.
"We are treating it pretty seriously," James said, but "we just have not found anything".
Three exceedances were also detected at Kaiteriteri Beach this season, which were traced back to human contamination from the stormwater outflow pipe that drains onto the beach.
One of the common more-serious disease-causing organisms, Campylobacter jejuni, was found at the pipe in April.
Councillor Christeen Mackenzie was also concerned about the readings and the potential impacts on children.
"That stormwater outflow pipe is like a magnet for children to go and play there. It's unbelievable, but that is the reality."
She wondered if the pipe could be extended further down the beach and into the water so that even at low tide its outflow would not be played in.
However, the council's group manager community infrastructure Richard Kirby said extending the pipe would be costly and "impractical" given consenting, maintenance, and stability issues.
There were no alarm exceedances at Kaiteriteri Beach for 11 of the last 20 years.
However, five of the last seven years recorded exceedances - with four of those years recording more than one exceedance - including two "particularly high" results from this season, indicating that water quality is worsening at the beach.
In good news, it has now been two years without any alarm exceedances in Pōhara which James indicated could be related to the recent fixing of a sewer pipe in the community.
The council had also received several complaints about water clarity and colour in the Lee River.
Testing has shown that the river is still healthy, and invertebrates both upstream and downstream of the sampling site at Meads Bridge show no significant difference.
James suggests that forestry activity in the area, and the construction of the Waimea Community Dam - which maintained a high level of compliance while it was being built - might have impacted on the water's clarity and colour.
"Hopefully that is now going to be on the up with the dam now constructed," he said.
Beach water quality tends to be the highest on the incoming tide and people are advised not to swim during nor within 48 hours of rain.
Local Democracy Reporting is local body journalism co-funded by RNZ and NZ On Air.