As water quality and availability decreases in many parts of the world, salinity is becoming a major challenge that reduces crop yield, even in soilless cultivation systems. Therefore, novel strategies are needed to promote plant salt tolerance in these systems. We hypothesized that the non-essential element silicon (Si) and plant-growth promoting Bacillus spp. can alleviate salt stress of cucumber (Cucumis sativus L.) grown in hydroponics. We tested this hypothesis by growing cucumber seedlings with and without salt stress (75 mM NaCl) and with and without 1.5 mM Si and an inoculum of six rhizosphere Bacillus species in a full-factorial design. Seedlings were grown in a climate room for two weeks in independent deep-water culture containers. The applied salt stress strongly reduced plant biomass, whereas Si application under salt stress resulted in a substantial increase in cucumber shoot and root biomass. This beneficial impact of Si was also observed in increased plant height, leaf area, specific leaf area, root length, specific root length, root surface area and root volume. The Bacillus species increased root dry weight, specific leaf area as well as specific root length. In seedlings grown under salt stress, Si application increased shoot and root Si concentration, whereas Cl− concentration was reduced in the plant shoots. A reduction in Cl− concentration of the shoots was also apparent in the Bacillus treatment. Under non-stress conditions, neither Si nor Bacillus species affected plant growth parameters. However, shoot mineral content was affected as Si application reduced shoot Cl−and Ca2+ concentrations, and inoculation with Bacillus species decreased K concentration. We conclude that Si does promote salt stress alleviation during the early growth stage of cucumber grown in deep water culture and this has implications for soilless crop production. Seed inoculation with Bacillus species showed a beneficial trend for some plant growth characteristics and nutrient status under high salinity, although not as pronounced as for Si.