Mr Morris, who farms near Clydevale, said it was a widespread problem, and he and other Otago farmers did not want to pollute waterways or fall foul of the Otago Regional Council's dairy-effluent rules, but were unsure what to do.
Jeff Donaldson, group manager of Otago Regional Council-owned Regional Services, said his staff would be "reasonable" with farmers' plights, but would not tolerate effluent entering waterways.
"We're not going to be unreasonable, but clearly we believe responsibility rests with landowners to manage their effluent wisely."
That could involve using tankers to empty ponds or irrigating it on to areas such as shelter belts.
The council would continue to inspect farms and investigate breaches, Mr Donaldson said.
Mr Morris said most years he would be applying effluent to his pasture by now, but that was not possible, as winter was particularly wet and the soil had had no opportunity to dry.
Building bigger ponds was also not an option now, but it raised the question of just how big the ponds needed to be.
Environment Southland has suspended all compliance enforcement on dairy farms in the worst-hit areas of the province, although inspections were continuing north of Gore.
The council's director of environmental management, Warren Tuckey, said compliance officers were instead involved in advising farmers how to manage full effluent ponds and its land sustainability team in how to deal with dead stock.
Normally, dead stock are buried in offal pits, but with saturated ground conditions, there are no suitable areas for mass burials.
Mr Tuckey said burning was also not an option but burying in shallow trenches could be an option on some farms.
The council had also stopped posting invoices to rural ratepayers for the duration of the emergency.
In other developments, South Otago farmers are now dealing with a feed shortage, an issue which extends well beyond the southern part of the region hit hardest by a week of snow, wind, rain and freezing temperatures last week.
Dairy farmers yesterday attended the first of four field days organised by DairyNZ in Otago this week designed to help them to manage their way through what could become a significant problem just a month before cows are mated.