Although the risks of engineered nanomaterials (ENMs) to human and the environment are poorly understood, over 1800 consumer products currently on the market contain at least one ENM and the list continues to grow. The use of many of these consumer products will lead to direct release of ENMs into natural aquatic systems and several studies have demonstrated that ENMs can have adverse ecological effects. It is therefore important to understand the fate of ENMs in aquatic systems in order to predict and/or investigate their environmental implications. Microorganisms are abundant in natural waters into which they also release exudates such as soluble extracellular polymeric substance (sEPS). However, studies on how microorganisms and sEPS influence the fate and transformations of ENMs in natural waters are rare. In this doctoral research, sEPS were extracted from freshwater and marine phytoplankton (an important class of microorganisms) and their effects on the environmental fate of a variety of ENMs—including carbon nanotubes, copper and its oxides, iron, and titania nanomaterials—were studied. Interactions between algae, sEPS and ENMs were investigated via electron microscopy with energy dispersive X-ray spectroscopy, electrophoretic and dynamic light scattering, UV-Vis spectroscopy, X-ray diffraction, and infra-red spectroscopy. Effects of sEPS were investigated by studying changes in physicochemical properties, aggregation and sedimentation kinetics, and transformation of ENMs. The major components of sEPS were polysaccharides and proteins; and the ratio of both components varied with species and age of organism, as well as the nutrient composition of growth media. sEPS contained charged functional groups, such as carboxyl, phosphoryl, carbonyl, hydroxyl, amide, etc. Evidences for direct interactions (physisorption and chemisorption) between algae/sEPS and ENMs, mediated by the various functional groups on proteins and nucleic acids or phospholipids were found. Adsorption of sEPS to ENMs changed the size and surface charge of the particles. In addition, the attachment efficiencies of ENMs decreased in the presence of sEPS due to electrosteric stabilization. Impacts of algae and sEPS were also found on ENMs’ dissolution, transformation, and toxicity. This study demonstrated that the presence of phytoplankton and EPS in natural waters will have unique and important impact on the fate, transport, transformation, and effects of ENMs.