The potential risks of antibiotics in the environment have been increasingly recognized in their influence on ecosystem stability (directly affecting the microbial ecosystem) and human health. Abtibiotics occur at a trace level (micro-pollution) in environmental matrices such as waste water, surface water, groundwater, sediments and soils. Although they were initially used against microbial infections of humans and domestic animals, antibiotics are now widely used as growth promoters in agricultural production (e.g. poultry, livestock, and fish farming). Given the overuse or misuse for non-therapeutic purposes, in particularly with the rapid increase in food animal production, the types and concentrations of antibiotics in environmental matrices have dramatically increased. This review summarizes our knowledge of antibiotic sources and residual concentrations in the environment (water, soil, and sediment) and their adverse effects on microbial communities and functions. Antibiotics are released into the environment after uses in human and veterinary medical treatments and in animal husbandry and fish farming, and via applications of contaminated manures or slurry as fertilizers to agriculture soils. Six groups of massively produced antibiotics have been detected in environmental matrices (especially in urban sediment, water, and sludge), including macrolides, fluoroquinolones, sulfonamides, tetracyclines, penicillins, and others (like trimethoprim). Residual concentrations of antibiotics vary with environmental matrix type: with trace level found in surface water (μg/L), levels at μg/kg in soils, and higher concentrations ranging from μg/kg to mg/kg in sediments. Residual concentrations of antibiotics in sediments depend on type, discharge amount, sediment properties, and other environmental factors. Antibiotics are redistributed in the environment matrices via processes of sorption-desorption, transport, and degradation, etc. Environmental factors, such as clay content, organic matter, and iron oxides in soil and sediment, and pH, dissolved organic carbon (DOC), and cations, have been found to influence movement of antibiotics in environmental matrices. Degradation processes for environmental residual antibiotics include hydrolysis, photolysis, and biodegradation. Biodegradation is a ubiquitous process for antibiotics degradation in environmental matrices while hydrolysis is the typical process for antibiotics degradation in water. The movement and degradation processes of environmental residual antibiotics are predominantly determined by the type of antibiotic, with multiple processes usually contributing to their redistribution and degradation. Adverse effects of environmental residual antibiotics were revealed, including reducing microbial biomass and activity, altering microbial community structure and diversity (especially functional microbial community, such as nitrifiers and denitrifiers), changing microbially-mediated ecological processes (such as nitrification and denitrification), and inducing antibiotic resistant microbial community in contaminated environments. Antibiotic resistance genes for tetracycline, chloramphenicol, vancomycin, erythromycin, sulfonamides, methicillin, and β-lactams have been well studied in environmental matrices. Antibiotic resistant genes have also been identified in pathogens due to long term overuse or misuse of antibiotics, such as the super bacteria (MRSA), and have led to major public health concerns. Further studies of the disturbances and influences of antibiotics on ecosystem functions and services (including public human health) as well as effects of multiple contaminations of antibiotics with heavy metals and other organic pollutants in environmental matrices are required. The type and chemical structure of antibiotics should be taken into account for understanding their ecosystem disturbances while high-throughput quantitative analytical methods are under development.