"We're just having to go a wee bit deeper. If they've got a big enough well than we're able to go to a submersible type pump, otherwise they've had to go to new wells."
An Environment Canterbury spokeswoman said wells up to 20m deep, mostly in the Selwyn Waihora zone, were being affected.
She said while irrigation contributed to the situation, groundwater levels were very low this summer after three consecutive winters with little rainfall to replenish the aquifers.
"There are full irrigation restrictions on all takes from the Selwyn River," the spokeswoman said.
"Many groundwater takes are on partial restriction and all deep groundwater takes have restrictions on their annual volumes. This has been the situation since November 2015."
District councillor Debra Hasson recently sought answers from ECan after six shallow wells downstream from Lincoln University's Ashley Dene farm had gone dry within two months of a new 160m bore on the farm coming into operation.
Cr Hasson wanted to know why the university was granted consent in 2014, when the zone was already over-allocated.
ECan team leader for consents Sam Beaumont said the university had simply transferred an already consented water allocation from one bore, near the corner of Springs Rd and Gerald St, to the new Ashley Dene bore.
"Every time someone comes to do that, we make sure we are not giving out any more water over the year, that they are taking the same volume they always have," Mr Beaumont said.
However Cr Hasson said the new bore was taking water from the Silverstream drainage catchment which connected to the dried up wells and Coes Ford, whereas the university's previous allocation had taken water from the L2 drainage catchment.
The ECan spokeswoman said it was difficult to say whether the operation of the Ashley Dene bore could have affected the downstream wells.