Our project is located in an semi-arid climate area with low precipitation and high evapotranspiration rates, where the rain water will be captured and used in water closets.
The subsurface groundwater is unsuitable for human use because it has high levels of nitrates due to sewage contamination. The non potable water test analisys was conducted according to the local law requirements and every year it must be retested. Furthermore, since the nitrates are dissolved, they can not be removed with conventional treatment, only with high-cost reverse osmosis membrane treatment.
We will use only draught resistant and native plants for landscape which reduced considerably our water demand for irrigation.
But a backup irrigation system is still needed and we consider using groundwater, because it is not a potable source, not suitable for human use even after treatment and it is highly recommended for plants since nitrate is a natural fertilizer.
The irrigation water would then naturally infiltrate back into the soil, the nitrates are absorbed by the plants helping cleaning the groundwater and closing the cycle.
Would this strategy be acceptable for achieving Water Efficient Landscaping, WEc1?

Disclaimer: about one year ago we did exactly this same question throught the leed online feedback an the answer that we had was the following:

Thank you for contacting the Green Building Certification Institute. Note that in this forum we cannot approve project teams' strategies, only offer guidance. The LEED reference guide, as well as multiple LEED Interpretations (LIs), suggest that your strategy would not be accepted by the review team. For example one LI, which can be reviewed by searching our LI database (available through this link https://www.usgbc.org/LeedInterpretations/LILanding.aspx) for entry number 456, discusses that "Although the local groundwater at the project may not be suitable for drinking straight out of the ground, it still represents an important source of potable water. Using groundwater as an irrigation source does not achieve this credit."

This being said, it may be possible that your strategy would be accepted as an Innovation in Design (ID) credit. This is because, as you mentioned, the nitrates would be a good fertilizer and the process to make the water potable would be excessive. Also the CIR mentioned above was written for NCv2.0, not for NCv2009. Therefore, we recommend you submit a CIR to have your strategy pre-approved as an ID credit. A CIR ruling is guaranteed to be accepted by the review team. For more information regarding CIRs refer to this website http://www.gbci.org/Certification/Resources/cirs.aspx. When submitting your CIR we recommend mentioning the elaborate process for making the water potable, the benefit of the water to the vegetation, etc.

However, the reference guide states that potable water meets or exceeds EPA’s drinking water quality standards and is approved for human
consumption by the state or local authorities having jurisdiction; it may be supplied from wells or municipal water systems.

Before submitting a CIR dont you think we still can follow by this way once is proven that our ground water is not potable?