Phytopathogenic fungi infections, such as those caused by Rhizoctonia solani, result in significant yield losses in several economically important crops. To enhance biological control strategies, three aquatic bacterial strains were isolated from drinking water sources i.e. Pantoea agglomerans B1, Serratia plymuthica B2 and Proteus mirabilis B3 were evaluated in vivo against R. solani in flax and cotton. The infection-inhibition effect of three biocontrol agents was tested in glasshouse and field experiments. In flax, the bacterial strains demonstrated varying effects on seedling survival and technological characteristics. A positive correlation was observed between seedling survival (stand) and straw yield, along with its components. Among the tested strains, Serratia plymuthica B2 and Pantoea agglomerans B1 showed the highest efficacy under both glasshouse and field conditions compared to the untreated control. In cotton, the greatest disease suppression was achieved by strain B2, followed by strains B1 and B3 in both seasons, compared to the untreated control. The highest yield increases (kentar/feddan) were recorded as 5.342 and5.158 (B2), 5.005 and 4.911 (B1), and 4.644 and 4.394 (B3) during the 2023/2024 seasons, respectively. Finally, in glasshouse experiments, all bacterial biocontrol agents either completely or significantly limited seedling mortality in flax and reduced disease incidence in cotton seedlings caused by R. solani. Among them, strain B2 proved to be the most effective biocontrol agent. This study concludes that these bacterial strains, particularly B2, can be recommended as part of an integrated system for controlling R. solani, thereby improving straw yield quality in flax and increasing cotton yield.