Pharmaceutical contamination of surface water is a serious concern, posing a threat to the ecosystem stability. This study focuses on assessing the occurrence and environmental impact of diazepam and its active metabolites oxazepam, temazepam and nordazepam in two Czech rivers, identifying the main sources of pollution, and evaluating the effectiveness of root-zone wastewater treatment plant in removing these contaminants. Benzodiazepines were detected in 72% to 100% of the water samples, with oxazepam concentrations peaking at 67.50 ng/L, particularly at the conventional wastewater treatment plant effluent. While root-zone plants are often reported to be effective in removing organic pollutants, the investigated plant failed to effectively remove oxazepam, likely due to insufficient maintenance. Ecotoxicological assessments revealed that multiple sites exhibited hazard quotient values of moderate to high environmental risk, suggesting the persistence and bioaccumulative nature of these contaminants. The findings highlight the limitations of current wastewater treatment technologies in fully eliminating benzodiazepines, which continue to be detected even after treatment, leading to potential long-term ecological consequences. This research calls for the development and implementation of more effective, scalable, and cost-efficient wastewater treatment solutions to reduce pharmaceutical pollution, and for an ongoing monitoring of aquatic environments to protect freshwater resources and safeguard biodiversity.