Niwa has conducted the first nationwide assessment of river fragmentation, looking for structures that can act as barriers to fish.
Freshwater ecologist Dr Paul Franklin said these structures were often human-made and included dams, culverts and weirs.
The assessment found that New Zealand had some of the highest densities of barriers to fish passage in the world, with about 0.16 barriers per kilometre.
"This works out at a minimum of 48% of the river network being at least partially inaccessible to migratory fish, and a further 36% that could be restricted but has not yet been assessed for risk to fish passage," Dr Franklin said.
In Otago and Southland, 5254 structures on the river network were assessed.
Nearly 60% of Otago’s network had barriers to fish migration and about 25% of Southland rivers had barriers.
"Otago has some large dams on big rivers so that takes out long reaches of river."
Dr Franklin said the fragmentation of river systems was a key driver of freshwater biodiversity loss.
"There are just over 50 native New Zealand fish species, with around 85% of those not existing anywhere else in the world," he said.
"Many of our iconic fish, such as eels and the whitebait species, migrate between the sea and our rivers to complete their life cycle.
"However, they often encounter different structures along the way that act as a barrier, stopping them reaching key habitats.
"This ultimately leads to lower abundances and potentially loss of these species."
He said some of the dams in Otago had fish traps which catch fish down stream, and then they are manually transferred over to the top side, and visa versa.
But there were many other obstacles that made it difficult for fish to travel upstream.
To address this challenge, he said Niwa was studying the swimming abilities of fish and coming up with solutions to help them migrate.
"We put fish into the equivalent of a water treadmill to see what speed they can maintain — we want fish to be able to move upstream casually, not having to fight the whole way," he said.
"We can then assess what adjustments need to be made to structures in our river networks to help fish pass through these environments more easily."
Culverts, for example, alter the flow of a stream or river and affect the ability of fish to swim through them.
"You can install baffles into culverts, which are basically panels placed inside the tube that help to slow water down and create resting areas, so that fish can pass through into the stream above.
"It’s small changes like this that can make a big difference.
"If we don’t start addressing the threats that we’ve placed into their environment, these precious fish will one day be gone," Dr Franklin said.
