The treatment of water is needed for the supply of adequate quality of drinking water and before the discharge of wastewater to the environment. Since the flocculants used in the water and wastewater plants have been shown to be potentially hazardous for the human health, it has become necessary to find flocculants less dangerous and more eco-friendly. This thesis consists of a systematic study to investigate the applications of natural submicron capsules (oil-bodies) and proteins extracted from oleaginous seeds for water treatment. Submicron capsules were extracted from different oleaginous sources and their flocculation activity has been investigated and characterized. We showed that they possess flocculation activity for clay suspensions comparable or even higher than the standard flocculants as alum and ferric salts. Moreover, the capsules have been tested for their ability to remove a range of pharmaceuticals from water. The investigation of oleaginous seed materials was further extended to the extraction of soluble proteins from press-cakes, the by-product of seeds after oil extraction. Thus, the flocculation activity of extracts from several press-cakes has been tested and compared to conventional flocculants, for example, alum and ferric salts. Finally, since lab-scale flocculation tests are usually off-line, in order to improve this methodology an on-line quantification method was developed. To do that, a typical jar test apparatus was equipped with six turbidity probes connected to a computer to get online measurements.