Due to their increased production and use, engineered nanoparticles are expected to be released into the aquatic environment where particles may agglomerate. The aim of this study was to explore the role of agglomeration of nanoparticles in the uptake and expression of toxicity in the rainbow trout (Oncorhynchus mykiss) gill cell line, RTgill-W1. This cell line was chosen as model because it is known to be amenable to culture in complete as well as greatly simplified exposure media. Nano-sized tungsten carbide (WC) with or without cobalt doping (WC-Co), two materials relevant in the heavy metal industry, were applied as model particles. These particles were suspended in culture media with decreasing complexity from L15 with 10% fetal bovine serum (FBS) to L15 to L15/ex, containing only salts, galactose and pyruvate of the complete medium L15. Whereas the serum supplement in L15 retained primary nanoparticle suspensions, agglomerates were formed quickly in L15 and L15/ex. Nevertheless, scanning electron microscopy (SEM) coupled with energy dispersive X-ray (EDX) elemental analysis revealed an uptake of both WC and WC-Co nanoparticles into RTgill-W1 cells irrespective of the state of agglomeration of nanoparticles. The localisation seemed to be restricted to the cytoplasm, as no particles were observed in the nucleus of cells. Moreover, reduction in cell viability between 10 and 50% compared to controls were observed upon particle exposure in all media although the pattern of impact varied depending on the medium and exposure time. Short-term exposure of cells led to significant cytotoxicity at the highest nominal particle concentrations, irrespective of the particle type or exposure medium. In contrast, long-term exposures led to preferential toxicity in the simplest medium, L15/ex, and an enhanced toxicity by the cobalt-containing WC nanoparticles in all exposure media. The composition of the exposure media also influenced the toxicity of the cobalt ions, which may dissolve from the WC-Co nanoparticles, with cells reacting much more sensitively toward cobalt ions in the absence of FBS. However, the toxicity observed by ionic cobalt alone did not explain the toxicity of the WC-Co nanoparticles, suggesting that the combination of metallic Co and WC is the cause of the increased particle toxicity of WC-Co. Taken together, our findings indicate that minimal exposure media can lead to rapid agglomeration of nanoparticles but that agglomeration does not prevent uptake into cells and the expression of toxicity.