Forward osmosis (FO) membranes have been used for wastewater recovery and desalination as a promising technology. This research studies the natural organic matter (NOM) fraction causing fouling on the active (AL) and support layer (SL) of a FO membrane, with the active layer facing the feed side (AL-FS), using a secondary wastewater effluent (SWWE) as feed water, and seawater as a draw solution (DS). Liquid chromatography with organic carbon detection (LC-OCD) chromatograms and fluorescence excitation-emission matrixes (F-EEM) spectra of the initial and final DS and SWWE suggested that protein-like substances and polysaccharides present in the SWWE were forming a fouling layer on the AL of the FO membrane, reducing the flux of water permeating through the membrane. NOM fouling shows a 90% reversibility when air scouring for 15 minutes within the concentrated feed water (CFW) is applied. When chemical cleaning of the AL (Alconox solution and EDTA) was performed after the former air scouring, the flux increased by 3%, and the irreversible fouling was quantified as 8.2%. Transparent exopolymer particles (TEP) were identified on the support layer of the FO membrane in contact with the seawater, reducing the flux of the FO membrane in ≤ 8.2% of the initial flux. Chemical cleaning of the SL with a solution of 1% NaOCl during 10 minutes was effective in removing the TEP accumulated on the membrane.