Mesoporous silica engineered nanomaterials are of interest to the industry due to their drug-carrier ability. Advances in coating technology include using mesoporous silica nanocontainers (SiNC) loaded with organic molecules as additives in protective coatings. The SiNC loaded with the biocide 4,5-dichloro-2-octyl-4-isothiazolin-3-one (DCOIT), i.e., SiNC-DCOIT, is proposed as an additive for antifouling marine paints. As the instability of nanomaterials in ionic-rich media has been reported and related to shifting key properties and its environmental fate, this study aims at understanding the behaviour of SiNC and SiNC-DCOIT in aqueous media with distinct ionic strengths. Both nanomaterials were dispersed in (i) low- (ultrapure water—UP) and (ii) high- ionic strength media—artificial seawater (ASW) and f/2 medium enriched in ASW (f/2 medium). The morphology, size and zeta potential (ζP) of both engineering nanomaterials were evaluated at different timepoints and concentrations. Results showed that both nanomaterials were unstable in aqueous suspensions, with the initial ζP values in UP below −30 mV and the particle size varying from 148 to 235 nm and 153 to 173 nm for SiNC and SiNC-DCOIT, respectively. In UP, aggregation occurs over time, regardless of the concentration. Additionally, the formation of larger complexes was associated with modifications in the ζP values towards the threshold of stable nanoparticles. In ASW, SiNC and SiNC-DCOIT formed aggregates (<300 nm) independently of the time or concentration, while larger and heterogeneous nanostructures (>300 nm) were detected in the f/2 medium. The pattern of aggregation detected may increase engineering nanomaterial sedimentation rates and enhance the risks towards dwelling organisms.