The performance of a full-scale photobioreactor (PBR) for the treatment of olive washing water (OWW) was evaluated under different HRTs (5–2 days). The system was able to treat up to 3926 L OWW day−1, and consisted of an activated-carbon pretreatment column and a tubular PBR unit (80 tubes, 98.17 L volume, 2-m height, 0.25 m diameter). PBR was an effective and environmentally friendly method for the removal of phenols, COD, BOD5, turbidity and color from OWW (average efficiencies 94.84 ± 0.55%, 85.86 ± 1.24%, 99.12 ± 0.17%, 95.86 ± 0.98% and 87.24 ± 0.91%, respectively). The diversity of total bacteria and microalgae in the PBR was analyzed using Illumina-sequencing, evaluating the efficiency of two DNA extraction methods. A stable microalgae-bacteria consortium was developed throughout the whole experimentation period, regardless of changes in HRT, temperature or solar radiation. MDS analyses revealed that the interplay between green algae (Sphaeropleales), cyanobacteria (Hapalosiphon) and Proteobacteria (Rhodopseudomonas, Azotobacter) played important roles in OWW bioremediation.