This study aimed to characterize the impact of organic and inorganic compounds in the feed solution on the membrane fouling and the boron flux in a forward osmosis (FO) membrane system. Lab-scale FO membrane systems were operated in batch mode, with a solution containing organic compounds (humic acid (HA), bovine serum albumin (BSA), sodium alginate (SA)), scaling constituents (calcium chloride, sodium sulfate), and boric acid as feed solution, and with concentrated sodium chloride as draw solution. Preparations of membrane sample for scanning electron microscopy and energy dispersed spectroscopy (SEM-EDX) by freeze- and by oven-drying showed different results and can therefore not be considered as suitable for the evaluation of the samples. Results showed that the organic fouling layer did not have an impact on water and boron fluxes, but reverse salt flux (RSF) was reduced in the presence of BSA and HA. The molar flux ratio between water and boron was roughly 105, regardless of the presence of the fouling. The hydrophobicity and surface charge of the fouling layer were not related to the boron transport rate. A thicker and more uniform organic fouling layer, as observed, caused a reduced RSF. The organic compounds in the feed solution impeded the crystallisation of gypsum, which can lead to reduce scaling.