The Regional Council's Plan Change 6, designed to be paired with the Ruataniwha water storage scheme, is now in place and, by 2020, all rivers and streams in the Tukituki catchment must be fenced.
Cattle are routinely seen in the Tutaekuri, Ngaruroro and Tukituki rivers.
Ms Bowers said the "handful of farmers" who had little regard for the wellbeing of the Tukituki and other rivers should be changing their farming practices now.
Federated Farmers Hawke's Bay president Will Foley agreed.
"We should fast-track the practice and not wait for deadlines - we just need to get on and do it."
In some areas a considerable investment in fencing was needed.
"We can't expect it to happen overnight but we need to get on and get it done," Mr Foley said.
Sitting regional councillor Rick Barker said a regulatory framework was needed even though farmers knew it was "the right thing to do".
Fencing all waterways was "a way off", he said. "The regional council can't just click its fingers and impose new rules - it needs to go through a process."
Former regional councillor Murray Douglas had been lobbying for stricter controls for years and, in 2013, successfully moved that it become proactive about removing stock from waterways.
A staff report said council would put up fences where it could, such as on council-controlled edges, but it was "hit and miss".
Mr Douglas said it was ridiculous. In many parts of New Zealand, fencing stock from waterways was mandatory along with a "hard-nosed" approach to breaches.
A regional council spokesman reiterated that the Tukituki River was "highly unlikely" to be the source. However, it had not been completely dismissed.
Even if E. coli was observed in the river - typically at a low level when found - groundwater samples taken between the river and Hastings District Council bores had no E.coli present, he said.
The Tukituki River water moved toward the district council's water-supply bores. It took months, years or decades to travel the 2.5km or so. The long travel time through the aquifer sediments cleaned E.coli from the groundwater, he said.
"E.coli is better able to survive in groundwater than campylobacter. Both are indicators of faecal contamination. If no E. coli is seen, it is extremely unlikely that campylobacter is present."
Regional council interim chief executive Liz Lambert said an "extraordinary monitoring programme" was continuing for at least three weeks.
From Monday last week, the regional council introduced a weekly water monitoring programme instead of monthly for this time of year, collected sheep and cow faeces to investigate potential contamination sources, undertook catchment modelling, interviewed landowners on farming practices and worked to establish a clear weather picture leading up to the outbreak, now said to have affected 4700 people.
"All of these activities - from the dirty work of collecting poo to desk-top catchment modelling - will help us to understand what happened and why, and to take precautions so that it doesn't happen here again," she said.
Hastings District Council has decided to chlorinate all its water supplies "for the foreseeable future".
