Per- and polyfluoroalkyl substances (PFAS) are persistent contaminants, with emerging compounds such as perfluorobutane sulfonate (PFBS) and perfluorobutane sulfonamide (FBSA) increasingly detected in aquatic ecosystems. Effects on aquatic organisms, however, remain poorly understood. We conducted a chronic exposure study to assess species-specific stress responses in Dreissena polymorpha and Corbicula sp. Bivalves were exposed to PFBS or FBSA across environmentally relevant to extreme concentrations. Mortality, behavioural endpoints (valve movement, burrowing speed and depth, attachment rate), and physiological responses (respiration) were measured. Mortality was low for PFBS (LC50 > 100 mg/L for both species) but higher for FBSA (LC50 = 37.8 mg/L for Corbicula sp.; 0.14 mg/L for D. polymorpha), indicating greater FBSA potency and higher sensitivity of D. polymorpha. Attachment probability of D. polymorpha was unaffected by exposure level but lower in PFBS-exposed individuals (40.6%) than in FBSA-exposed ones (62.3%). At the highest PFBS concentration, Corbicula sp. burrowed deeper, suggesting a stress response. Burrowing depth was unaffected by FBSA, likely due to 100% mortality at the highest concentration. Valve movement response variables (N = 30) were grouped into principal components to reduce collinearity. Overall, the majority of behavioural variability could be explained by differences between species, whereas PFAS-induced effects were generally subtle, concentration-dependent, and species-specific. Treatment effects were more consistently observed in Corbicula sp. than D. polymorpha. Oxygen consumption of both species increased significantly with increasing body mass, but there was no significant effect of PFAS type and exposure concentration. Overall, PFBS triggers behavioural responses, whereas FBSA is more lethal. Our findings highlight the value of behavioural and physiological endpoints to detect sub-lethal stress and reveal species-specific responses to emerging PFAS in aquatic ecosystems.