Small bioreactor platform (SBP) capsules are designed to implement selective bacterial cultures within aquatic media, mainly wastewaters, in a bioaugmentation process. Such capsules, coated with cellulose acetate (CA) membranes to form three‐dimensional (3D) structural barriers, are intended to provide a long‐term protected and confined environment for the introduced bacterial cultures. These state‐of‐the‐art 3D membranes allow the tailored design of the encapsulated bacteria and adjustment to several environmental properties, such as organics and nutrients, pressure, and the natural flora. Our study characterizes, for the first time, the mechanical and thermal properties of the SBPCA structural membrane and the effects of water molecules on these properties. High‐resolution scanning electron microscopy images of the CA membranes show mesh‐like porous structures, crucial for mass transport both inside and outside the capsule. Thermal gravimetric analysis shows a reduction of ~115°C in the thermal decomposition temperature of wet capsules compared to that of dry capsules. Mechanical testing shows that the modulus and maximum stress of wet samples are each decreased by an order of magnitude compared to those of dry samples at similar maximum strain. The permeability of the CA membrane to phenol, a model water organic pollutant, was found to be 3 × 10−8 cm2 s−1. It is concluded that water molecules soften CA structural membranes, yielding soft amorphous structures, which are needed for the optimized processing of the SBP capsule. The plasticizing effect is important in the membrane architecture formation and fiber elasticity when used in an aqueous environment.