The biofilm phenotype offers bacterial communities protection from environmental factors, as evidenced by its role in the viability, persistence, and virulence of cells under conditions in which flow is present, such as in riverbeds, industrial piping networks, and the human circulatory system. Here, we examined the hypothesis that temperature-an environmental factor that affects the growth of the Gram-positive bacterium Staphylococcus epidermidis-controls, through dual mechanisms, persistence of this bacterial strain in a shear environment characteristic of the human circulatory system. We demonstrated that temperature and antibiotics impact the surface-adhered biofilm and material disseminated downstream in different ways. Specifically, by means of three-dimensional (3D) confocal and scanning electron microscopy, an increase in surface-adhered biofilm heterogeneity was observed with increasing temperature. Additionally, we found a 4-log decrease in cell viability at the biofilm surface as the perfusate temperature was increased from 37°C to 50°C. Finally, the viability of cell-containing fragments that were disseminated from the substrate was assessed by downstream sampling, culture, and optical density measurement. We found that although temperature decreased the viability of the surface-adhered biofilm, the downstream material remained viable. And yet, in the presence of antibiotics, the growth of disseminated material was nearly completely inhibited, even though the addition of antibiotics had no significant impact on the viability of the surface-adhered biofilm. The mechanism involves both biofilm structural damage, as quantified by morphology of debrided material, and reduced cell viability, as quantified by assay of bacterial cells present in the surface-adherent biofilm and in the downstream effluent. The results potentially identify parameter ranges in which elevated temperature could augment current antibiotic treatment regimens.IMPORTANCE Bacterial biofilms are a leading cause of medical device infections. Staphylococcus epidermidis is commonly responsible for these types of infections. With increasing occurrences of antibacterial resistance, there has been a new push to explore treatment options that augment traditional antibiotic therapies. Here, we show how thermal treatment can be applied to both degrade bacterial biofilms on substrates and impede the proliferation of cells that detach from them. Understanding the response of both surface-adhered and dispersed bacterial cells under thermal stress conditions is a foundational step toward the development of an in situ treatment/remediation method for biofilm growth in medical devices; such an application could use oscillatory flow of heated fluid in a catheter as an adjuvant to antibiotic treatment. The work furthermore provides new insight into the viability of disseminated biofilm material.