This study investigates the effects of Nd:YAG laser irradiation combined with different irrigation protocols on the marginal seal of root fillings. Limited information exists regarding the effects of morphologic changes to root canal (RC) walls after Nd:YAG laser irradiation after smear-layer removal with EDTA on the sealing ability of root fillings. The 75 root-filled teeth (5 × 15 teeth) were analyzed for through-and-through leakage by using capillary flow porometry (CFP). The RC cleaning procedure determined the assignment to a group: (1) irrigation with NaOCl 2.5% and EDTA 17% or standard protocol (SP), (2) SP + Nd:YAG lasing (dried RC), (3) NaOCl 2.5% + Nd:YAG lasing (dried RC), (4) SP + Nd:YAG lasing (wet RC), or (5) NaOCl 2.5% + Nd:YAG lasing (wet RC). Groups 1r to 5r consisted of the same filled teeth with resected apices up to the most apical point of the preparation length. Resection was performed after the first CFP measurement. Roots were filled with cold lateral condensation. CFP was used to assess minimum, mean flow and maximum pore diameters after 48 h, and immediately after these measurements, including root resection. Statistics were performed by using nonparametric tests (p > 0.05). An additional three roots per group were submitted to SEM of the RC wall. Through-and-through leakage was observed in all groups. Statistically significant differences were observed in maximum pore diameter: 1r > 3r, and 1r > 5r; in mean flow pore diameter: 1r > 2r, 2r < 4r (p < 0.05). Typical Nd:YAG glazing effects were observed when the smear layer was present and exposed to the laser fiber (i.e., in the groups without use of EDTA) or when the fiber tip made direct contact with a smear-layer free RC wall. The reduction in through-and-through leakage is significantly higher with the Nd:YAG laser as smear-layer modifier than when smear layer is removed with an EDTA rinsing solution.