In this study, for the environmental development, the antifungal, antibacterial, and antioxidant activities of a water extract of flowers from Acacia saligna (Labill.) H. L. Wendl. were evaluated. The extract concentrations were prepared by dissolving them in 10% DMSO. Wood samples of Melia azedarach were treated with water extract, and the antifungal activity was examined at concentrations of 0%, 1%, 2%, and 3% against three mold fungi; Fusarium culmorum MH352452, Rhizoctonia solani MH352450, and Penicillium chrysogenum MH352451 that cause root rot, cankers, and green fruit rot, respectively, isolated from infected Citrus sinensis L. Antibacterial evaluation of the extract was assayed against four phytopathogenic bacteria, including Agrobacterium tumefaciens, Enterobacter cloacae, Erwinia amylovora, and Pectobacterium carotovorum subsp. carotovorum, using the micro-dilution method to determine the minimum inhibitory concentrations (MICs). Further, the antioxidant capacity of the water extract was measured via 2,2′-diphenylpicrylhydrazyl (DPPH). Phenolic and flavonoid compounds in the water extract were analyzed using HPLC: benzoic acid, caffeine, and o-coumaric acid were the most abundant phenolic compounds; while the flavonoid compounds naringenin, quercetin, and kaempferol were identified compared with the standard flavonoid compounds. The antioxidant activity of the water extract in terms of IC50 was considered weak (463.71 μg/mL) compared to the standard used, butylated hydroxytoluene (BHT) (6.26 μg/mL). The MIC values were 200, 300, 300, and 100 µg/mL against the growth of A. tumefaciens, E. cloacae, E. amylovora, and P. carotovorum subsp. carotovorum, respectively, which were lower than the positive control used (Tobramycin 10 μg/disc). By increasing the extract concentration, the percentage inhibition of fungal mycelial was significantly increased compared to the control treatment, especially against P. chrysogenum, suggesting that the use of A. saligna flower extract as an environmentally friendly wood bio-preservative inhibited the growth of molds that cause discoloration of wood and wood products.