How do we manage the supply of ground water when using boreholes to improve water retention, to ensure the water supply is sustainable?

Difficult to answer generally, it is a very borehole / aquifer specific question.

The first step has to be to build an understanding of the groundwater body that you are exploiting, so that estimates can be made about sustainable yields and long term water quality. This will also allow an optimisation of abstraction (in terms of volumes and numbers of boreholes and potential interaction with neighbouring schemes, saline water bodies etc).

Gather as much information about the setting (hydrogeological, geological, physical, historical use etc) of the abstraction scheme as possible and build a simple model (qualitatively to start with) of the borehole and use that model to predict likely yields, catchment zones and what might influence ongoing abstraction / use.

Boreholes drilled / installed speculatively, with little background info will always be subject to uncertainty in terms of quality, quantity and sustainability. Boreholes that have fallen into disuse / failed are however, also very useful in building your model of the locality and assisting in the installation of more successful / sustainable supply boreholes.

Hope this is helpful.