Soil and water loss is one of the most severe kinds of land degradation, particularly in drought-vulnerable regions. It diminishes fertility and increases natural catastrophes, such as floods, landslides, sedimentation, drought, and economic, social, and political issues. The current study explores the efficacy of individual and combination cyanobacteria and bacteria inoculation on runoff production from plots generated by rill erosion on soil from the Marzanabad drought-prone region, northern Iran, and exposed to five successive rainfalls with three days intervals. Experiments were conducted on mid-sized plots with dimensions of 6 × 1 m, three replications, and a 30% slope during simulated rains at the lab with an intensity of 50 mm h−1 and a duration of 30 min. Also, excess runoff of about 2.180 L min−1 was introduced to the plots to promote rill formation. Because none of the treated plots created runoff during the design rainfall, the expected circumstances were subject to continuous rainfall until runoff was generated. Compared to the control plots, statistical analysis indicated that the study treatments had a significant (p < 0.01) lower influence on hydrological components during the initial rainfall event. The highest performance was obtained in the combination inoculation of cyanobacteria and bacteria in successive rainfalls (i.e., first to the fourth event), which reduced runoff volume and coefficient by 35.41, 45.34, 26.35, and 36.43%, respectively. During subsequent rainfalls, the bacteria and combination treatment of cyanobacteria and bacteria did not vary substantially (p = 0.94) on the study components. As a result, after consecutive rainfall events, runoff volume dropped by 20.79, 22.15, 12.83, and 15.87%, and the runoff coefficient reduced by 20.80, 22.15, 12.84, and 15.88%. The cyanobacteria treatment diminished the study components only after the initial rainstorm event. The current study’s findings underscored the need to minimize water loss in the early phases of erosion in drought-sensitive regions where soil and water conservation is a vital task.