Fish & Game ecologist Jayde Couper said surveys were carried out on Lakes Wakatipu, Wanaka, Hawea and Dunstan over five days, with a Fish & Game boat.
Zigzagging along precisely determined routes at various parts of the lakes, the sounder recorded fish at between 3m and 30m depths.
"We are relieved weather conditions for the survey were almost perfect, considering the unfortunate hammering the North Island was getting from Cyclone Gabrielle at the time," Mr Couper said.
Niwa previously conducted acoustic monitoring in the Southern Lakes in 2007, 2008 and 2009.
This year’s survey followed the same routes, to enable comparisons with previous data.
"Niwa will analyse the data on behalf of Fish & Game, and we look forward to seeing their draft report in a few months."
He said the acoustic surveys expanded on Otago Fish & Game’s other methods to monitor fish species, which included angler surveys, spawning surveys, drift dives, electric fishing, eDNA sampling, gill netting and analysing competition catches.
Potential effects of climate change, fish harvesting and water quality were not fully understood, and they hoped long-term monitoring, including that done by other agencies and groups, would add to that knowledge.
Mr Couper said Fish & Game had been monitoring freshwater fish and their habitats since the organisation’s inception more than 30 years ago.
"We are pleased to see other organisations taking a growing interest in the water quality of the Southern Lakes.
"We look forward to engaging with them further, sharing information to protect and improve water quality, and helping to ensure that people can continue to enjoy angling in these world-class lake fisheries."
Otago Fish & Game Council chairman Colin Weatherall said the Southern Lakes were among the most "highly sought-after fishing playgrounds" in the country.
"Fish & Game recognises the value of fishing and recreation in our lakes, which contributes millions of dollars to the economy.
"The benefits of fishing to people’s health and wellbeing are also well documented."
Mr Weatherall said the council had made it a strategic priority to determine drivers for changes in the trout and salmon populations, and to establish a long-term monitoring method for these amazing fisheries.
