How should we value water utilization in irrigated agriculture

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In our interest to make irrigated agriculture more efficient and sustainable we have approached the water transmission, distribution and application system in a manner to limit any 'waste' to the unaccounted for sinks. This has been done so successfully in some locations that there is very minimal leakage out of the system and the fields implementing deficit irrigation such that no deep percolation is entertained. Does this make our system really sustainable? This question is posed on the basis that our practices, especially in the arid and semi-arid regions have resulted into loss of groundwater recharge with the consequence that any existing groundwater wells are drying up, water tables are being lowered and salinity due to no leaching is increasing. In the long term would our advanced surface water utilisation be sustainable for both the soil and water resources in agriculture?