Lipid bilayer membranes have a native (albeit small) permeability for water molecules. Under an external load, provided that the bilayer structure stays intact and does not suffer from poration or rupture, a lipid membrane deforms and its water influx/efflux is often assumed negligible in the absence of osmolarity. In this work we use boundary integral simulations to investigate the effects of water permeability on the vesicle hydrodynamics due to a mechanical load, such as the viscous stress from an external flow deforming a vesicle membrane in free space or pushing it through a confinement. Incorporating the membrane permeability into the framework of Helfrich free energy for an inextensible, elastic membrane as a model for a semipermeable vesicle, we illustrate that, in the absence of an osmotic stress gradient, the semipermeable vesicle is affected by water influx/efflux over a sufficiently long time or under a strong confinement. Our simulations quantify the conditions for water permeation to be negligible in terms of the time scales, flow strength, and confinement. These results shed light on how microfluidic confinement can be utilized to estimate membrane permeability.