Reactions ranged from the jubilant to the cautiously positive.
Dr Smith announced his decision, using his powers under the Resource Management Act, after seeking the views of Environment Canterbury (ECan), applicants - Five Rivers Ltd, Southdown Holdings Ltd and Williamson Holdings Ltd - and others.
Dr Smith's decision means the consents will now be decided by a five-member board of inquiry named yesterday, rather than by an Environment Canterbury (ECan) panel which was due to hear the consents over 16 days starting from March 10.
Waitaki MP Jacqui Dean, who asked Dr Smith to call in the consents, said she was "very pleased".
"Like it or not, we have these proposals on our plate and the call-in will enable the best possible process to take place," she said.
Parliamentary Commissioner for the Environment Dr Jan Wright also welcomed Dr Smith's decision.
She told NZPA he was correct to identify that there were significant concerns over water quality.
"These proposals have national implications ranging from the special unique ecology of the Mackenzie, to tourism and carbon-free power generation," Dr Wright said.
Green Party co-leader Russel Norman claimed a victory for the Green Party on the decision, but Twizel resident Scott Aronsen, who was involved in a public meeting over the proposals, sounded a note of caution.
"It's great, but there's always a but," Mr Aronsen said.
While the board of inquiry would put another hurdle in front of the developers "it's not dead and buried yet", he said.
The board of inquiry includes Environment Court Judge Jane Borthwick, who has had extensive experience dealing with water issues in the Waitaki catchment, and three commissioners - Edward Ellison, Mike Bowden and James Cooke - at present on a four-member panel appointed by ECan to consider water applications for irrigation by the three dairy farm companies, along with more than 100 others in the Upper Waitaki catchment.
The fifth member is internationally recognised lake ecologist Prof David Hamilton, who studied at the University of Otago where he obtained his doctorate.
Dr Smith said he had deliberately chosen the members of the board of inquiry because of their expertise and included the three commissioners who were on the ECan panel.
That would ensure appropriate continuity of the decision-making process with the water applications tied to the effluent consents.
Dr Smith said yesterday he called in the 15 applications because they were "nationally significant" due to their scale, the fragile and special nature of the region, the importance of fresh water quality to the Government, and the high level of public interest.
Dr Smith said the call-in had been complicated because recent amendments to the Act did not apply.
Water resource consent applications, which date back to 2004 and were at present being heard by the ECan panel, also fell outside the amendments to the Act.
Issues of animal welfare - the cows in cubicles - raised by many submitters did not fall under the Act.
"This process will enable the most robust decision possible for these contentious issues," Dr Smith said.