Four days from next Monday have been set aside for hearings and sentencing for those who have admitted offending.
Most of the charges relate to the discharging of effluent on to production land causing either the ponding of effluent or its discharge into waterways - both breaches of the regional council's water plan.
Court sheets show the farmers come from throughout Clutha district including Clydevale, Milton, Kaitangata, Owaka Valley and Romahapa.
Council resource management director Dr Selva Selvarajah said the alleged offences were spotted during its routine annual monitoring of farms.
The Balclutha court prosecutions closely follow a series of fines imposed on North Otago dairy farmers in late April.
Three properties there were fined more than $48,000 in total.
Dr Selvarajah said recent prosecutions around the country showed the fines imposed ranged from $5000 up to $40,000.
After the North Otago cases, Dr Selvarajah told the Otago Daily Times the issue of non-compliance by dairy farmers had continued over several years.
The council had tried, through $750 infringement notices and other education-type means, to improve matters.
Last season, the council felt it was not making any huge improvement and decided to take a "hard stance" and prosecute.
Some prosecutions have been transferred to the Dunedin District Court.
