The persistence of biofilm-forming bacteria in drinking-water (DW) distribution systems poses a significant challenge to public health, particularly when conventional disinfection methods fail to ensure microbial control. Among the microbial processes that influence biofilm resilience, bacterial coaggregation—the specific recognition and adhesion between genetically distinct bacterial strains—has emerged as a key mechanism shaping biofilm structure and function. This study provides novel insights into how coaggregation enhances biofilm tolerance to sodium hypochlorite disinfection, using Stenotrophomonas maltophilia as a model emerging pathogen in DW systems. The key finding is that coaggregation with the strain 005P significantly increased biofilm resistance to high chlorine concentrations (>10× MBC), compared to both monocultures and non-coaggregating dual-species biofilms. This enhanced tolerance was associated with increased biofilm thickness, elevated levels of extracellular polymeric substances (EPSs), notably proteins and polysaccharides, and the formation of more compact, spatially uniform biofilm structures. These results highlight the role of coaggregation in enhancing biofilm tolerance by promoting EPS production, stabilizing the three-dimensional architecture, and providing physical protection against disinfectants. In particular, coaggregation with D. acidovorans 005P led to a more compact and uniform biofilm, indicating that interspecies interactions drive structural reorganization that contributes to chlorine resistance. These findings underscore the importance of microbial cooperation in biofilm persistence and offer valuable insights for optimizing disinfection strategies in DW systems.