The structure of microalgal extracellular polymeric substances (EPS) plays a key role in influencing the transfer and distribution of antibiotic resistance genes (ARGs) in livestock wastewater. This study investigated how lead stress and gibberellin stimulation affect microalgal growth, biomass composition, photosynthetic pigment content, pollutant removal efficiency, and ARGs dynamics within wastewater and different EPS layers. Low lead concentrations (1 mg/L) stimulated microalgal growth, whereas high concentrations (5 mg/L) inhibited it. Gibberellin alleviated lead-induced stress by increasing chlorophyll content (by 0.384 mg/L) and enhancing polysaccharide levels in both microalgal cells (by 0.895 mg/L) and EPS (by 3.382 mg/L), compared to lead stress alone. Lead exposure reduced the efficiency of nitrogen and COD removal and significantly altered the bacterial community, increasing the relative abundance of Pseudomonadota and redistributing bacteria from tightly bound EPS (TB-EPS) to soluble EPS (S-EPS). These changes were most pronounced in the TB-EPS layer. Additionally, lead stress promoted the proliferation and spread of ARGs, whereas gibberellin mitigated this trend by enhancing microalgal vitality and ARGs removal capacity. The findings offer new insights into optimizing microalgal systems for livestock wastewater treatment and controlling the environmental dissemination of ARGs.