Contamination of natural water (NW) by emerging contaminants has been widely pointed out as one of the main challenges to ensure high-quality drinking water. Thus, the effectiveness of a solar-driven free chlorine advanced oxidation process simultaneously investigating the elimination of six organic microcontaminants (OMCs) and three bacteria from NW at a pilot-scale was evaluated in this study. Firstly, the solar/free chlorine process was studied at lab-scale using a solar simulator to evaluate the effect of free chlorine concentration (0.5–10 mg L−1) on OMC degradation and generation of toxic oxyanions (e.g., ClO3− ions). Thus, the best free chlorine concentration observed was applied for the simultaneous removal of OMCs and pathogens under natural solar light at pilot scale. At lab-scale, the solar/free chlorine (2.5 mg L−1) process achieved 80% of total degradation in 5 min (1.4 kJ L−1 of accumulative UV energy) with an oxidant consumption of 0.3 mg L−1 and without ClO3− generation. Similar results were attained under natural solar irradiation at a pilot-scale. For all bacteria strains, the legally required detection limit (DL = 1 CFU 100 mL−1) for reclaimed water reuse was attained in a short contact time. Still, more importantly, the solar/free chlorine (2.5 mg L−1) process effectively avoided the possible bacterial regrowth in the post-treated sample after six days. Finally, the combination of free chlorine with solar irradiation provided a simple and energy-efficient process for OMC and bacteria removal in NW at a pilot-scale.