Aim: To compare shock wave-enhanced emission photoacoustic streaming (SWEEPS) with sonic- and ultrasonically activated irrigation systems in removing Enterococcus faecalis biofilm from the root canal system. Methodology: Fifty human single-canalled mandibular premolars were included in the study. After access cavity preparation, the root canals were prepared to a standardized size and taper. Then, the entire root surface was covered with two layers of resin, and the root apices were sealed before sterilization. All root canals were inoculated with E. faecalis biofilm, and the samples were incubated aerobically for 2 weeks at 37 °C. Biofilm formation was confirmed by scanning electron microscopy. All samples were randomly divided into five groups (n = 10 each) based on their irrigation activation method as A (no treatment or negative control), B (no irrigation or positive control), C (sonically activated irrigation (SAI)), D (ultrasonically activated irrigation (UAI)), and E (needle irrigation activated by an Er: YAG laser device using a SWEEPS quartz tip (SWEEPS)). Then, dentine chips were retrieved, vortexed, and diluted for colony-forming unit counts. Data were analysed using analysis of variance and post-hoc Tukey tests (α = 5%). Results: All methods could significantly reduce E. faecalis biofilm compared with control so that the UAI, SWEEPS, and SAI groups indicated a 23.54%, 14.89%, and 7.81% biofilm reduction, respectively. UAI demonstrated a significantly more effective reduction of E. faecalis biofilm than SAI (p = 0.004). Conclusions: All irrigation activation methods significantly reduced E. faecalis biofilm, with ultrasonic use being the most effective.