Two variants of layer-by-layer deposition of polyelectrolytes (polyacrylic acid and polyethyleneimine) for the encapsulation of low-molecular-weight hydrophobic substrates (carboxylic acid esters) were proposed. The spectrophotometric method was used to study the kinetics of alkaline hydrolysis of the esters by monitoring the permeability of microcapsule shells. The first procedure provides a preliminary microencapsulation of substrates into the carbonate matrix to form stable capsules 7–10 μm in size with a low wall permeability. According to the second procedure, the polyelectrolytes were adsorbed directly on the dispersed substrate. In this case, nanosized capsules are formed, whose permeability is controlled by the ultrasonic treatment and the number of deposited layers.