The effect of RO concentration on microbial ecosystem changes and the chemical composition of white wastewaters (WW; dairy effluents generated during the hydraulic flush of dairy processes), recovered from two dairy plants (A and B), was evaluated. The WW of dairy plant A was dominated by psychrotrophic bacteria, but no increase of the total number of 16S rRNA genes in the retentate throughout RO was obtained. A thermotolerant lactic acid bacteria genus, Streptococcus, was the most abundant genus in the initial samples of WW from dairy plant B. During WW recirculation in the RO system, the total number of 16S gene copies in the retentates generated by plant B increased significantly after 15 h. An adapted RO treatment with specific parameters is proposed to limit the growth of problematic bacterial genera, so promoting revalorization and reducing the environmental impact of WW dairy effluents.