Last week's discovery of the invasive alga didymo in Western Fiordland was a reminder of the importance of the preventive action, Mr Donaldson said.
To keep rivers such as the Taieri, and Stewart Island and the North Island free of the pest ''check, clean, dry'' was the best defence.
''There are about 180 affected waterways now but there are 500 in South Island so there are still a lot not affected.''
The ''check, clean, dry'' method was also the best defence against a range of freshwater pests, he said.
''We don't know where the next freshwater pest will come from. Our rivers are in a very susceptible pristine condition.''
Ministry for Primary Industries (MPI) senior adviser Sherman Smith said the Freshwater Pest Partnership Programme was a national approach to preventing the spread of freshwater pests, including didymo.
It was co-ordinated by MPI and involved the Department of Conservation, regional councils, Fish and Game, iwi and industry.
''It is focused on stopping the spread of freshwater pests through freshwater users taking personal responsibility for reducing the risk of spread through the `check, clean, dry' programme.''
The focus was on surveillance and advocacy around high-value sites such as Fiordland.
Research on preventing the spread was ongoing to better understand how didymo survived in certain environmental conditions, which might help to determine how to stop the spread and define areas of greatest risk, Mr Smith said.
Mr Donaldson, the regional council's representative on Freshwater Pest Partnership Programme, said claims birds or animals spread didymo were wrong.
Animals dried quickly and the oil on birds' feathers and their flight meant the risk of them spreading it was low. Didymo would be killed in the 40degC temperature of a bird's gut, he said.
''Our biggest concern is humans.''
That was highlighted by the six months it took for didymo to be found in the upper Clutha, after it was discovered in the Hawea River, Mr Donaldson said.
The ''check, clean, dry'' practice also helped prevent the spread of other freshwater pests, such as lagarosiphon, which could cause major problems for flood mitigation if it ever spread into Lake Wakatipu.
Another pest, hornwort, which choked waterways, had been eradicated from the South Island and keeping it out would require water users doing ''check, clean, dry'', he said.
