Microsieve membranes are microfabricated devices that possess a high and controlled porosity. Due to the extremely high product throughput, microsieves are very sensitive systems in terms of flux decline during clean water measurements. The goal of this investigation was to study the influence of the surface properties of silicon nitride microsieves and the hydrodynamic parameters on the clean water flux performance. First, we studied the properties of bare silicon nitride dices. Contact angles and XPS measurements clearly demonstrated that silicon nitride experiences aging and variations in its surface properties, making it necessary to hydrophilize and homogenize the substrates. To understand the role of the surface properties on the water permeation, the water flux through unmodified, hydrophilized and hydrophobized silicon nitride microsieves was studied as a function of the wetting procedure and the presence of air in the feed liquid. For most surfaces, a good wetting protocol and the exclusion of contaminating particles and air from the system led to stable fluxes. Hydrophobized membranes presented low performance when they were poorly wetted. In these cases, air was massively deposited on the surface, since the low working pressures made the filtration sensitive to air bubbles. For highly hydrophobized membranes (contact angle, θ = 112°) no stable fluxes could be measured due to rapid dewetting.