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Nowadays, the search for and development of new forms of materials with biocides is an actual problem of the modern science of nanosized materials due to the problem of microbiological contamination, which can be solved by using nanocontainers carrying biocides. Depending on the morphology of the nanocontainers and the filled active agents, it is possible to create coatings with specially designed self-healing functionality or multifunctional properties. The purpose of this work was to produce submicro-containers (SMCs) with a shell of SiO₂ nanoparticles and a core of polymerized 3-(trimethoxysilyl) propyl methacrylate filled with 5-dichloro-2-n-octyl-4-isothiazolin-3-one (DCOIT) in an oil in water (O/W) emulsion. The chemical nature of the individual components of the system and nano-capsules were investigated using NMR spectroscopy. The size and zeta potential of the SMCs were measured by a dynamic light scattering method (d = 170–180 nm, polydispersity index PDI = 0.125 and zeta-potential = 55 mV), the morphology of their outer surface was determined using SEM. The results of NMR analysis showed that during the addition of the biocide into the SMCs, its chemical structure is retained, as is its activity. Minor changes in the chemical shifts of the ¹H NMR spectra of the SMCs with DCOIT, as well as of the biocide itself, confirm the inclusion of DCOIT inside the SMCs.