The high boron (B) content in desalinated seawater is a concern for crop development. However, in spite of the importance of the soil microbial community in soil fertility, the below-ground impacts of B are still unknown. Here, in a soil-ryegrass model system, the activity, biomass and diversity of the soil microbial community were evaluated in response to irrigation with: i) 0.3 mg B L-1; ii) 1 mg B L-1; and iii) 50 mg B L-1. We assessed two different compounds of boron: boric acid (H3BO3) and disodium tetraborate decahydrate (Na2B4O7·10H2O). Overall, the 1 mg B L-1 dose was identified as the threshold limit that did not irreversibly harm soil sustainability. In contrast, the highest B dose had a noticeable impact on the nitrogen (N) cycle of the soil, as demonstrated by an increase in the water-soluble N content and a decrease in urease activity. Analysis of the phospholipid fatty acids (PLFAs) revealed that the effect of B on the soil microbial biomass was dependent on the chemical form used. High B doses reduced soil microbial respiration and influenced the composition of the bacterial and fungal communities, with fungal diversity being diminished, as revealed by sequencing approaches.