| Summary: | Under irrigation with saline wastewater, SO<sub>4</sub><sup>2−</sup>, Cl<sup>−</sup>, and Ca<sup>2+</sup> aggregated in the topsoil, and Mg<sup>2+</sup> was significantly higher in the deeper soil than in the topsoil and 40 cm soil layers. The abundance of <i>Zoopagomycota</i>, <i>Ascomycota</i>, <i>Mortierellomycota</i>, <i>Basidiomycota</i>, <i>Chytridiomycota</i>, <i>Rozellomycota</i>, <i>Blastocladiomycota</i>, <i>Monoblepharomycota</i>, <i>Mucoromycota</i> and <i>Olpidiomycota</i> in the surface soil was influenced by Mg<sup>2+</sup>, whereas Ca<sup>2+</sup> affected the abundance of <i>Zoopagomycota</i> and <i>Chytridiomycota</i>. In the 40 cm soil layer, Mg<sup>2+</sup> and Cl<sup>−</sup> promoted Actinobacteria, Proteobacteria, <i>Nitrospirae</i>, <i>Firmicutes</i>, <i>Entotheonellaeota</i>, <i>Myxococcota</i>, <i>Gemmatimonadota</i> and <i>Methylomirabilota</i>, whereas they inhibited <i>Planctomycetota</i>, <i>Acidobacteria</i>, <i>Chloroflexi</i>, <i>Patescibacteria</i> and <i>Bacteroidota</i>. In the 80 cm soil layer, SO<sub>4</sub><sup>2−</sup> and Cl<sup>−</sup> promoted <i>Rozellomycota</i>, <i>Mortierellomycota</i>, <i>Chytridiomycota</i>, <i>Ascomycota</i>, and <i>Mucoromycota</i>, but had a negative effect on <i>Glomeromycota</i>, <i>Blastocladiomycota</i>, <i>Olpidiomycota</i> and <i>Monoblepharomycota</i>. The increase in salinity significantly reduced the abundance of the <i>Actinomycetes</i> phylum and the <i>Amoebozoa</i> phylum. Both saprophytic and symbiotic fungi decreased with increasing salinity.
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