Fadnavis, who will complete four years in office tomorrow, stressed the scheme was "100 per cent successful"
and also accused the opposition parties of "politicising" the issue.
The chief minister averred the programme aims at creating structures to store rainwater through harvesting and not letting it percolate in the soil.
In the wake of deficit rainfall in the state (77 per cent of the annual average), ground water extraction was up by 27 per cent this season over last year in the state, resulting in depleting level subsurface, he argued.
"And when you extract water, the ground water level is going to fall. It will replenish when it rains next year," he said, while interacting with a select group of journalists at his official residence `Varsha' here late night Monday.
The chief minister observed that 179 talukas in the state received poorer rainfall vis--vis the monsoon of 2014.
Yet, 143 of them are such where the ground water level is better when compared to those in 2014, Fadnavis added.
He attributed the better levels in the talukas concerned to the implementation of the programme.
"One (the opposition) doesn't try to understand the science behind it...So, the issue is being merely politicised.
The scheme is 100 per cent successful," he said, without naming any party.
Seeking to drive home his point, Fadnavis said the government treated 16,522 villages under the programme, launched in 2015.
The chief minister said the government, with public participation, completed 5.57 lakh works worth Rs 7,692 crore.
"All these works have created 24 lakh TCM water, 10,694 works were carried out through public participation, we can see 45 per cent rise in productivity," he added.
The Congress and the NCP had last week attacked the government over the programme, alleging it was a "failure".
They had also claimed the scheme was implemented unscientifically and contracts were awarded to contractors close to those in power.
On his government's four-year performance, Fadnavis, the first BJP chief minister of the state, said it has done "huge qualitative and quantitative works in all areas".
Seeking to underscore the difference between his administration and the previous Congress-NCP government, the CM said his dispensation did better job in areas such as rural development, agriculture, irrigation, health, water resources, law and order, education, business, tourism and others.
"I am not claiming everything is fair. There are challenges (before the government). But the train of (growth of) Maharashtra had derailed, (and it) has been brought on track and it is running fast," Fadnavis said.