Many dissolved substances attach easily to sediment particles. In the presence of suspended sediments bioavailability of dissolved substances is therefore, usually reduced and clays are even applied to “wash” natural waters upon pollution. In organisms which feed on food organisms in the size range of these suspended sediment particles, however, bioavailability of such substances may even increase. For microorganisms the interaction with dissolved substances and suspended sediment particles so far has hardly been investigated. We specifically tested: (1) the importance of suspended particles as an uptake route for dissolved substances; and (2) the significance of particle surface properties, i.e. surface load and mineralogy. As a model system we used an axenically cultured strain of a widespread and often abundant flagellate (“Spumella-like” flagellate strain JBM10). We tested the toxicity of cadmium (II) and mercury (II) as well as availability of dissolved organic matter (DOM) in the absence as well as in the presence of different natural clays, i.e. a kaolinite, a montmorillonite, and a mixed clay, and of artificial silicate particles of different surface charge. When applied separately the presence of the heavy metals cadmium and mercury as well as of suspended particles negatively affected the investigated flagellate but nutritive organics supported growth of the investigated flagellate. Toxic stress response comprises behavioral changes including enhanced swimming activity and stress egestion of ingested particles and was generally similar for a variety of different flagellate species. In combination with suspended particles, the respective effect of trace metals and nutritive substances decreased. Regarding the particle quality, cadmium toxicity increased with increasingly negative surface charge, i.e. increasing surface density of silanol groups (Pearson's product moment, P = 0.005). For mercury particle mineralogy still had a significant effect (P < 0.001) but surface load seems to play a minor role and for nutritive organics no significant effect of the investigated particle properties was found. We conclude that: (i) flagellates are as sensitive as higher animals to heavy metal pollution; (ii) suspended particles decrease bioavailability of dissolved substances and ingestion of suspended particles probably play a minor role as uptake route for dissolved substances; and (iii) suspended sediment particle properties, i.e. surface charge and mineralogy, are key factors for the interaction between microorganisms and dissolved substances in the presence of suspended sediments.