The bacterial microbiome in aquaria plays an essential role in system stability by metabolizing toxic compounds like ammonia. This study monitored microbiome changes in seven zoo aquatic systems during their first year to assess responses to external influences. Over one year (October 2021–October 2022), water and swab samples were collected from one seawater tank and six filtration systems at regular intervals. Bacterial cultivation included total bacterial counts. Metagenomic analysis was performed on samples corresponding to environmental events using Oxford Nanopore sequencing. Taxonomical analysis at the phylum and genus levels used EPI2ME software. Diversity analyses and statistical tests were performed using R. Total bacterial counts increased steadily after inoculation and stabilized by the end of the collection period. Diversity analysis revealed significant differences within and between freshwater and saltwater tanks. Each aquarium exhibited a distinct bacterial community with frequent compositional changes. Despite environmental conditions and maintenance interventions and resulting disturbances that affected the microbiome, the overall nitrifying capacity remained unaffected. Nitrifying taxa emerged as potential indicators for environmental effects. Combined with investigations of ecological function, next-generation sequencing could facilitate the development of aquarium management protocols, ultimately improving fish welfare.