If the issue is dissolved salts coming from the irrigation water source (i.e., not primarily from the fertilizer) there are not a lot of options in flood floor systems because no leaching occurs with subirrigation. If the irrigation water electrical conductivity (EC) without fertilizer added is much above 0.7 mS/cm, using flood irrigation alone is difficult on long-term crops because ions accumulate in the root substrate.
The first priority with irrigation water that has a high EC is to try to purify the water (for example, reverse osmosis or blend with rain water). A periodic top watering with booms or hose can help to leach out salts and rebalance the nutrients in the root substrate. However, do not recycle the resulting runoff to the same crop because it is likely to have high levels of ions, such as sodium or chloride.
If the high EC is coming from over-application of fertilizer, and the EC of the irrigation water itself is low (0.7 mS/cm or below), there are more options. There is plenty of good research and grower experience that plants grown with flood irrigation can thrive with lower fertilizer rates compared with top watering because there is no leaching with subirrigation. For example, http://journal.ashspublications.org/content/118/6/771.full.pdf.
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