The usage of antibiotics in human as well as in veterinary medicine has increased immensely. Antimicrobial substances enter the environment daily from various sources, be it production, usage or disposal of waste products. They reach the water environment through sewer systems, waste water treatment plant outlet, and from animal and fish farms outlets. Through the use of livestock fertilisers and sewage sludge they reach agricultural lands. In soil their retention time is the longest. The fate of antimicrobial substances and their metabolites in the environment depends on their chemical properties and environmental characteristics, and the evolutionary and ecological characteristics of bacterial populations. It is determined by three important processes: adsorbtion, degradation and transfer in soil and aquatic environment. Antimicrobial resistant bacteria through horizontal gene transfer, genetic mutations and recombinations are influencing environmental resistance and can also contribute to the development of resistant pathogenic organisms, subsequently reducing antimicrobial medication treatment effectivity. The usage of properly pretreated manure plays a key role in reducing or completely eradicating the presence of veterinary-used antibiotics. Control, appropriate regulation and education of the general public about the prevention of human and veterinary antibiotics' entry into the enviroment are crucial for reducing ecological health risks, antibiotic presence in drinking water, plant biomass and in the food chain in general.