Although antibiotics have been used in large quantities for some decades, until recently the existence of these substances in the environment has received little notice. It is only in recent years that a more complex investigation of antibiotic substances has been undertaken in order to permit an assessment of the environmental risks they may pose. Within the last decade, an increasing number of studies covering antibiotic input, occurrence, fate and effects have been published. Antibiotics are one of the most important groups of pharmaceuticals. Antibiotic resistance is one of the major challenges for human medicine and veterinary medicine. However, there is still a lack of understanding and knowledge about sources, presence and significance of resistance of bacteria against antibiotics in the aquatic environment despite the numerous studies performed. This review summarizes this topic. It names important open questions and addresses some significant issues which must be tackled in the future for a better understanding of resistance related to antibiotics in the environment.