This study investigates the potential of bioaugmentation with Bacillus species to enhance wastewater treatment and develop a bacterial–CaCO3 system for self-healing cement applications. Utilizing microbiologically induced calcium carbonate precipitation (MICP), this study evaluates the dual functionality of Bacillus licheniformis and B. muralis strains. For wastewater treatment, the bioaugmentation process achieved significant pollutant reductions, including a 99.52% decrease in biochemical oxygen demand (BOD5), a 92.13% reduction in chemical oxygen demand (COD), and a substantial removal of heavy metals and nutrients. This process also produced high concentrations of CaCO3 precipitate enriched with viable bacterial cells, demonstrating an eco-friendly approach to improving water quality. For self-healing cement applications, bioaugmented CaCO3 crystals were coated with nutrient and sodium silicate layers to form a bacterial–CaCO3 coupled system. This system demonstrated a 92% recovery in compressive strength after 180 days, highlighting its ability to autonomously repair microcracks in cement-based materials. The layered encapsulation strategy ensured bacterial viability and a controlled activation mechanism, offering a scalable and sustainable solution for infrastructure resilience. This dual-function approach addresses critical environmental and construction challenges by linking efficient wastewater treatment with innovative self-healing material development, contributing to global sustainability and circular economy goals.