Note that the $2.25 per million litres, but this doesn't restrict Nestle to how many millions of litres they can pump.
The bigger issue is the unfairness in the value of water being charged for residential users versus industrial/commercial users. That unfairness is pushed even further when Nestle seeks to make a massive fortune off an essentially free resource. If we assume Nestle sells a 1L bottle of water for $2, the $2.25 per million litres they've paid results in $2 million in revenue. Sure, there's the issue of salaries, bottling costs, etc, that have to be accounted for, but let's not pretend Nestle's not getting the sweet end of the deal on this.
It is a zero-sum resource; water doesn't just appear in the aquifer at the same rate it's pumped out. Look at Southern California for an excellent example of this. It takes a long time for rainwater, for example, to reach the aquifer. Just because one lives in a region of heavy rainfall doesn't mean aquifer levels are consistently "safe" or "full". Any new industry tapping into an aquifer taxes it, and I think residents feel that those industries should be charged accordingly for the impact such industry has on the local water supply. Personally, I think that's fair.
Now, herein lies the rub: what's considered "fair value" for the resource? I think the residents have a distorted view of what that fair value is, since they pay more than what Nestle will. Residential water service is EXPENSIVE (laying pipe, maintenance, pumping stations, water treatment, etc), whereas the initial capital cost for a bottling plant is high, the company pays all costs for filtration, treatment and on-site infrastructure. Those costs are passed to the consumer, whereas residential water service is passed on to the residents. I don't know how the numbers compare, and $2.25 per million litres of water may, in fact, be fair market value for commercial/industrial use.
My concerns are more with respect to taxing the water supply for residents and local ecosystems. Generally, governments tend to have little regard for such impacts, thinking that because Canada has more lakes than all other countries combined that water is an infinite resource. That's not a good stance for making policy, either.