Antibiotic pollution in natural water bodies has reached alarming levels, posing a significant threat to the delicate balance of aquatic ecosystems. Bacteria and phytoplankton are foundational components of these ecosystems, playing crucial roles as decomposers and primary producers, respectively, and their symbiotic relationships are essential for maintaining ecological stability. Despite accumulating research focusing on the direct toxic effects of antibiotics, disruptions of complex bacteria-phytoplankton symbioses remain largely underexplored. In this review, we first introduce the symbiotic mechanisms between bacteria and phytoplankton, highlighting the processes underlying the formation of these relationships. We then examine the antibiotic sensitivity of bacteria and phytoplankton, highlighting the heightened vulnerability of bacteria. Finally, we explore the mechanism by which antibiotics disrupt bacteria, leading to altered interactions with phytoplankton. These disruptions cause shifts in phytoplankton population community structure and dynamics with implications for ecosystem functions, including a higher risk of exacerbation of harmful algal blooms. Our study reveals that even if environmental concentrations of antibiotics do not directly impact phytoplankton populations, they can affect phytoplankton populations and communities by altering symbiotic bacteria. Understanding bacteria-phytoplankton symbioses is thus essential for unraveling the ecological impacts of antibiotics. This underexplored field demands greater attention from pollution ecology researchers, as it is key to defining environmental thresholds for pollutants.