In addition to chemical factors, physical conditions also play a key role in the growth of microalgae. In this study, solid sediment in rivers was simulated by pure quartz sand with different particle sizes and the physical effects of disturbance rate, solid–liquid ratio and particle size on the growth of Chlorella vulgaris (C. vulgaris) were investigated through orthogonal analysis and response surface methodology (RSM) during co-cultivation of C. vulgaris and sediment. The result of ANOVA in orthogonal analysis showed that the effect ability of a single factor on biomass can be ranked as disturbance rate > particle size > solid–liquid ratio, 100 r/min disturbance rate and 30–40 M particle size are the most significant at the 0.05 level. Furthermore, the specific growth rate can reach 0.25/d and 0.27/d, respectively. With the growth of C. vulgaris, the pH of the solution reached a maximum of 10.7 in a week. The results from the RSM showed that strong interactions are reflected in the combinations of disturbance rate and solid–liquid ratio, and disturbance rate and particle size. Ramp desirability of the biomass indicates that the optimum levels of the three variables are 105 r/min disturbance rate, 0.117 g/mL solid–liquid ratio and 30–40 M particle size. In this case, the biomass can grow seven times in a week with 0.27/d specific growth rate and a pH value of 7–10.4. This study shows that the growth of C. vulgaris can be regulated by changing physical conditions simultaneously, and the optimization of physical conditions can be applied to biomass production, algae prediction and acid water treatment in rivers, lakes and reservoirs.