The indiscriminate use of antibiotics has brought the threat of resistance to this type of medicine, making diseases considered common a threat to public health. As every microorganism has defense strategies to escape imminent risks, obviously the microorganisms targeted by these medicines would find ways to defend themselves against their actions. Antibiotic resistance can be accompanied by resistance to heavy metals, which further worsens this alarming situation. Checking which genes are linked to these two types of resistance is very important for studies aimed at mitigating the negative effects caused and developing new medications. The present study investigated the microbial resistance profiles to antibiotics and metals in sediments from Guanabara Bay (RJ) and Lake Airo (AM) in Brazil. The coexistence of heavy metal and antibiotic resistance in both locations highlights the importance of resistance co-selection, which can result in multidrug-resistant bacteria. The persistence of heavy metals in the environment and their ability to exert selective pressure on microbial communities represent a significant threat to public health. Therefore, implementing effective heavy metal pollution control measures is crucial to mitigate the risks associated with antimicrobial resistance.