Antibiotics and their transformation products (TPs) make up a critical class of emerging contaminants. While parent compounds are frequently monitored, their metabolic derivatives often bypass detection due to analytical gaps and a lack of systematic risk assessments. This review evaluates the persistence, bioactivity, and ecological impact of antibiotic TPs across ecosystems. Our review illustrates the biotic and abiotic pathways of TP formation, showing that these metabolites often retain or amplify the bioactivity of their parent compounds. We elucidate how subinhibitory concentrations of TPs induce physiological stress, quorum sensing disruption, biofilm formation, and fundamental biogeochemical cycling, and how chronic exposure to trace levels of TPs drives antimicrobial resistance. To address these risks, we advocate for integrating improved wastewater treatment with advanced analytical frameworks, including non-target screening and multiomics approaches. We propose the implementation of TP-specific risk assessments and green antibiotic design to mitigate the global escalation of such risks.