Some of these low quality sites, such as the Clive River and Waipatiki Lagoon, have been on the council's radar for years and were still below safety standards.
Hawke's Bay Regional Council chairman Rex Graham said there was a real need for change.
"Clearly I am not happy about the state of some of our rivers, and this has become a real focus for our council."
The most pressing concern for human illness at fresh water sites is the level of E. coli, commonly found in human and animal poo. At coastal sites, it's a similar, but different bug - Enterococci. The likely source of the Havelock North gastro crisis was sheep poo which was washed into a pond during heavy rain.
Hawke's Bay Regional Council's resource management lead Iain Maxwell said the council was committed to cleaning up of the region's fresh and recreational water sites.
He said they've investigated four of the five sites above but haven't quite got to the bottom of the contaminant source.
"We are aware there are some sites that have had long standing issues with E.coli contamination," Mr Maxwell said.
"Our investigations at Wairoa River at ski club and the Clive River at the boat ramp show there are multiple sources of contamination, and we haven't been able to identify the primary source.
"Our investigations at Waipatiki Lagoon and Waipuka at Ocean Beach show it is related to wild fowl (geese), of which both ourselves and PanPac have undertaken eradication in both areas."
He said the council is currently looking at the Esk River case.
Mark Venman, regional manager of Hawke's Bay Fish & Game, said Hawke's Bay rivers, lakes and streams should be clean so locals can swim, fish and gather food.
"There is no doubt the region has some hard work to do to make that happen. The growing public concern about the state of our waterways shows that firm leadership and action is now required and our organisation is committed to working constructively with the region's local government bodies to make that happen."
Mr Maxwell said the council recently launched a $1 million plan to "kick-start" the clean up of six "environmental hot spots" around the region.
"The six hot spot areas are Lake Tūtira, Ahuriri estuary, Whakaki Lake and Wairoa River, Lake Whatuma and Tukituki catchment, Karamū Stream, and the Coastal Marine Environment," Mr Maxwell said.
He said other initiatives, including riparian planting along river and lake banks, farm stock exclusion from waterways and trapping sediment before it entered waterways.
"Protecting and improving our environment is a long-term project, which involves a range of initiatives and help from everybody."
When summer does arrive and the thought of swimming doesn't induce a shudder, it may pay to check the regional council's website for a steer on where to go if you don't want to get sick. Scientific testing begins again in November.