Trihalomethanes (THMs) are toxic disinfection by-products, formed in the reaction of chlorine with organic matter. This work aimed to study THM formation during a unique case study of managed aquifer recharge (MAR) with chlorinated desalinated seawater. THM formation was tested in the field, along a 3.0 m deep vadose zone gallery. Two small-scale experiments were conducted in the site, with untreated and with bromide spiked desalinated seawater. These were accompanied by a large-scale, ~1-month long operational MAR event. In the small-scale experiments, THM concentrations were shown to increase with bromide concentrations, with increasing dominance of the brominated species. Nevertheless, concentrations remained within the single µg/L range, which is an order of magnitude lower than drinking water regulations. Such low THM concentrations were also determined in the large-scale event. In both cases, THM formation occurred in the ponding water, without significant formation or degradation in the upper 3.0 m of the vadose zone. This study shows that MAR with chlorinated (<0.5 mg/L) desalinated seawater through sandy infiltration basins does not pose a threat to drinking water quality at this site.