Fungal contamination presents a persistent challenge in wastewater treatment and related sectors, including healthcare, agriculture, and pharmaceutical industries. In this study, the antifungal potential of electrochemically reactive nanobubbles (ERNBs) was systematically investigated against Candida albicans. The proposed mechanism involves ROS-mediated oxidative stress as the primary mode of fungal inactivation. ERNBs at varying concentrations were evaluated for antifungal efficacy by assessing fungal viability, extracellular leakage of biomolecules, and morphological alterations using field-emission scanning electron microscopy (FE-SEM). The results demonstrated that higher ERNB concentrations (∼108 bubbles/mL) led to near-complete fungal deactivation, accompanied by significant protein leakage, DNA release, lipid peroxidation, and severe membrane disruption. Fluorescent assays confirmed the generation of hydroxyl radicals (OH⋅) and hydrogen peroxide (H2O2) as the dominant ROS. A minimal amount of chlorine species was also detected in the ERNBs solution. Cytotoxicity tests on human dermal fibroblasts revealed minimal adverse effects, indicating the high biocompatibility of the ERNBs. These findings demonstrate that ERNBs can serve as a safe, effective, and promising disinfection strategy for fungal control in water treatment and other biocontaminated environments.