Antimicrobial resistance (AMR) has emerged and spread globally. Recent studies have also reported the presence of antimicrobials in a wide variety of aquatic environments. Conducting a nationwide monitoring survey of AMR in the environment to elucidate its status and to assess its impact on ecosystems and human health is of social importance. In this study, we developed a novel high-throughput analysis (HTA) system based on a 96-well plate solid-phase extraction (SPE), using automated pipetting and an SPE pre-treatment system. The effectiveness of the system as an HTA for antimicrobials in environmental water was verified by comparing it with a conventional manual analytical system in a domestic hospital over a period of two years and four months. The results of the manual analysis and HTA using a combination of automated pipetting and SPE systems were generally consistent, and no statistically significant difference was observed (p > 0.05) between the two systems. The agreement ratios between the measured concentrations based on the conventional and HTA methods were positively correlated with a correlation coefficient of r = 0.99. These results indicate that HTA, which combines automated pipetting and an SPE pre-treatment system for rapid, high-volume analysis, can be used as an effective approach for understanding the environmental contamination of antimicrobials at multiple sites. To the best of our knowledge, this is the first report to present the accuracy and agreement between concentrations based on a manual analysis and those measured using HTA in hospital wastewater. These findings contribute to a comprehensive understanding of antimicrobials in aquatic environments and assess the ecological and human health risks associated with antimicrobials and antimicrobial-resistant bacteria to maintain the safety of aquatic environments.