The cultivation of vegetables in greenhouses requires seedlings produced in nurseries with high levels of practice specialisation. The nurseries are dedicated to the early stages of growth, from sowing to the first leaves. There, the seeding density and the hydro-climatic conditions favour diseases. Plant protection treatments are carried out with the use of low-cost machines, whose efficiencies and safety conditions depend on the workers’ ability. The irrigation system with a mechanised horizontal spray boom could be an alternative solution to the hand-held spray gun. This research aimed to investigate the use of a horizontal boom sprayer for the distribution of pesticides in different pressure conditions and forward speeds compared with a spray gun, in relation to tomato growth stages. The tests were carried out on tomato seedlings grown in polystyrene seeding boxes and arranged on hanging benches. Deposits on the seedlings (µL cm−2) and losses in the soil (µL cm−2) were assessed by means of standard colorimetric analysis. In order to reduce the environmental pollution and increase the sustainability of the treatments, the pressure at the horizontal spray boom should be reduced and the arrangement of the outermost nozzles may also be better set on the boom.