The aim of the study was to investigate the disinfecting efficacy of a standardized irrigating solution activated by ultrasonics or laser irradiation on mature dual-species biofilms at different root levels in vitro. Conventional access cavity preparations were done on 160 single-rooted mandibular premolar teeth with single canals. Freshly extracted oral microbial strains of Staphylococcus aureus, Streptococcus mutans, Enterococcus faecalis, and Candida albicans after biochemical confirmation were used to generate two discrete dual-species microbial inoculums. The sterilized tooth samples were randomly segregated into two groups (n = 80) and inoculated with a mixed inoculum of S. aureus + E. faecalis strains (Group 1) and S. mutans + C. albicans strains (Group 2), respectively. Following the 21-day incubation period under aerobic conditions, the infected specimens in each group were divided into four subgroups (n = 20) and subjected to experimental treatment protocols. This included a positive control (no treatment of biofilms), syringe irrigation alone with TruNatomy needle, passive ultrasonically activated irrigation with 20# Irrisafe tip, and laser agitation of irrigant with Er,Cr:YSGG laser using RFT 2 laser tip. Root canals of experimental specimens (except the control samples) are instrumented with TruNatomy rotary file system using 1:1 mixture of 3% NaOCl and 18% etidronic acid as irrigants. The quantitative assessment of reduction in viable biofilm microbes after treatment was done using colony-forming unit counts and confocal laser scanning microscopy image analysis. The obtained data were analyzed statistically with a significant level set at 0.05. Laser-assisted irrigation has shown a considerably higher mean percentage reduction of microbes compared to ultrasonic agitation and the syringe irrigation showed the least microbial reduction (P = 0.001). No significant difference was noted between the three root regions of ultrasonic and laser groups (P > 0.05), whereas in the syringe groups, apical portions showed higher microbial counts compared to cervical and mid-root regions (P = 0.001). Erbium laser-assisted irrigation has performed superior to ultrasonic agitation against both the experimental dual-species biofilms, while the syringe irrigation showed the least microbial reduction specifically at apical root portions.