Aquatic environments have been affected by the increase in bacterial resistant to antibiotics. The aim of this review is to describe the studies carried out in relation to the bacterial population structure and antibiotic resistance genes in natural and artificial water systems. We performed a systematic review based on the PRISMA guideline (preferred reporting items for systematic reviews and meta-analyzes). Articles were collected from scientific databases between January 2010 and December 2020. Sixty-eight papers meeting the inclusion criteria, i.e., “reporting the water bacterial community composition”, “resistance to antibiotics”, and “antibiotic resistance genes (ARG)”, were evaluated according to pre-defined validity criteria. The results indicate that the predominant phyla were Firmicutes and Bacteroidetes in natural and artificial water systems. Gram-negative bacteria of the family Enterobacteraceae with resistance to antibiotics are commonly reported in drinking water and in natural water systems. The ARGs mainly reported were those that confer resistance to β-lactam antibiotics, aminoglycosides, fluoroquinolones, macrolides and tetracycline. The high influence of anthropogenic activity in the environment is evidenced. The antibiotic resistance genes that are mainly reported in the urban areas of the world are those that confer resistance to the antibiotics that are most used in clinical practice, which constitutes a problem for human and animal health.