Council's parks team leader Wendy Bainbridge said groundwater was common in graves throughout New Zealand.
"It has always been a factor in parts of Whanganui cemeteries including Aramoho," she said.
A double-depth grave (1.8m) was more likely to have water in the bottom than a single-depth grave (1.6m) but it did happen, particularly during a very wet winter.
Bainbridge said caskets were lowered to the top of the water level and water was pumped out of the gravesite before the casket was fully lowered.
The gravesite was then backfilled with soil immediately.
"We do now ensure that the equipment for filling the grave is removed from the site to prevent family members using it before the water is pumped," she said.
"This is an accepted way of dealing with this issue throughout a number of cemeteries in New Zealand. This is normally explained to the family by the funeral director prior to the committal."
tevens said that was not enough.
"They're trying to remedy the situation by pumping it out for one minute," he said.
"They're saying it's acceptable to put people in water. I'm saying it's not acceptable."
Colin Leslie said his partner's father was also "put in a pond of water" when he was buried last year and they also only found out about the problem at the burial.
"I could see the water in the bottom of the hole," Leslie said.
"It's just ridiculous. Who wants to be buried in a pond? It just beggars belief really, it's disgusting.
"I don't think a lot of [the new area] has been used. They either have to look at another area to develop or do some proper investigation."
The council also said draining groundwater as a more permanent fix could require resource consent and a wastewater solution because of human waste contaminants.
Stevens said the situation was "obscene" but was not a reflection on cemetery staff.
"We've got to look at the big picture, this is not about me," he said.
"But [the council has] to be honest and upfront about the service standard that they're providing.
"What I'm saying is, do people find this acceptable to have their loved ones buried in water knowing that they are going to decompose in water and go into the ground?"
Stevens said he would have made different decisions around his son's burial if he had known.
"I'm not prepared to lay down on this issue," he said.
Bainbridge said the sexton had reviewed the process "and we are satisfied that our practices are sound".