Lake Wanaka was slightly different from the other two lakes, in that the salmon preferred to live at a lower depths, for some reason.
"It just seems to be something they do for whatever reason and it can sometimes mean they can be hard to find."
At this stage there was no need to be worried, Mr Halford said.
Fish and Game would carrying out surveys of fish numbers in the lake during the summer and would also be talking to local anglers about what they had noticed.
"We will be concentrating efforts and talking to anglers to see where they are fishing."
"Hopefully, they will bring up some salmon and we can look at their condition."
Fish and Cruise Lake Wanaka owner operator Alan Baxter said he had noticed a considerable decline in the number of salmon he was catching.
"I haven't caught a salmon in ... at least two years whereas, not too long ago, I caught more than 200 in a month."
Mr Baxter had his own theory as to why salmon had become more scarce in the past few years.
"My theory is they have left because they can't stand the lake snow in their gills.
Obviously, that's just my theory but I think there's a connection."
The decline in the number of salmon caught followed a similar timeline to the spread of lake snow, he said.
Mr Halford said nobody was sure what effect lake snow had on the fish but it was something that needed to be investigated.
Other fish, such as rainbow and brown trout, did not seem to be affected, he said.
"We will just try and do a bit of a brief survey about what people fishing on the lake are seeing in terms of lake snow, which hopefully, will give us a bit of a better picture of what is happening."
