Excessive exposure to heavy metals is known to induce deleterious effects on health. The monitoring of heavy metals in sewage is important for examining environmental pollution induced by treated sewage effluent (TSE). In the current investigation, heavy metals concentrations of TSE of two sewage treatment plants in the Jazan region of KSA were monitored using a Perkin Elmer Optima 7000 DV inductively coupled plasma optical emission spectrometer (ICP-OES). The heavy metals concentrations were below the permissible limit, according to the Ministry of Water and Electricity (MWE) standards of Saudi authorities, except for magnesium and mercury. TSE from the treatment plants was subjected to additional treatment using the volatile organic compounds (VOCs) of the bacterial strain Citrobacter freundii. A marked reduction of the heavy metals concentrations of the bacterial-treated TSE was recorded. The impact of the bacterial-treated TSE on germination indices of Vigna radiata and Hordeum vulgare was investigated. The seedlings irrigated with the bacterial-treated TSE recorded a clear enhancement of growth parameters. Moreover, the level of accumulated heavy metals in seedlings irrigated with bacterial-treated TSE was reduced compared with those irrigated with untreated TSE. The current study clarified that the level of heavy metals in TSE could be markedly reduced via the application of bacterial VOCs and hence it can be used as a water resource for agricultural purposes.