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The programme is carried out by Land Information New Zealand, in conjunction with local councils and community groups, and represents an ongoing government investment of more than $600,000 a year to control lagarosiphon and hornwort in specific New Zealand lakes.
''Both species of weed represent a very real threat to the health of New Zealand's lakes,'' Land Information Minister Maurice Williamson said.
''Lake Wanaka is a good example of there being noticeably less lagarosiphon this year when compared to 2012. A combination of suction dredging, hand weeding and herbicide control has been used by divers at the lake.''
The Lake Wanaka Lagarosiphon Management Committee - comprised of Linz, the Guardians of Lake Wanaka, Department of Conservation, Otago Regional Council and the Queenstown Lakes District Council - is eight years through a 10-year lake weed control and reduction plan.
Linz Crown property manager Bill Naik said achievements at Lake Wanaka included clearing lagarosiphon from Paddock Bay and Bishops Bay. Overall, lagarosiphon had been contained to the south end of the lake.
''As a result we're proposing to reduce the size of our containment area, by moving the containment line approximately 6km towards the south end of the lake,'' Mr Naik said.
Linz expected to assess Lake Wanaka's 10-year management plan next year to consider an ongoing strategy for the future management and control of lagarosiphon in the lake.
The timing of Linz's lagarosiphon control work is dependent on several factors, including weather and water conditions, which can affect the success of the work.
At Lake Benmore, unusually high rainfall this year has limited control work. Monitoring is planned for later this year to help determine what level of further control work is required and where.
The focus for Lake Dunstan is on controlling lagarosiphon in areas of high use.
''We've successfully kept these areas, such as boat ramps located around the lake, clear of lagarosiphon,'' Mr Naik said.
''The main aim of this control programme, and others, is to reduce the risk of transmitting lagarosiphon to other lakes, as well as ensuring high-use areas are kept clear for recreational users.''
Originally used by the aquarium trade, lagarosiphon was first noticed in the Rotorua lakes in the 1950s. The unwanted organism, which is capable of choking waterways, smothering native aquatic plant communities and establishing quickly if untreated, has gradually appeared in many lakes.
Hornwort is a submerged freshwater weed that rapidly invades water of varying clarity, temperature, light and nutrient level. Its dense growth crowds out native species and impedes irrigation, drainage and other water uses.