Wastewater Treatment Plants (WWTP) are a major repository and entrance path of nanoparticles (NP) in the environment and hence play a major role in the final NP fate and toxicity. Studies on silver nanoparticles (AgNP) transport via the WWTP system and uptake by aquatic organisms have so far been carried out using unrealistically high AgNP concentrations, unlikely to be encountered in the aquatic environment. The use of high AgNP concentrations is necessitated by both the low sensitivity of the detection methods used and the need to distinguish background Ag from spiked AgNP.In this study, isotopically enriched 109AgNP were synthesized to overcome these shortcomings and characterized by a broad range of methods including transmission electron microscopy, dynamic and electrophoretic light scattering. 109AgNP and gold NP (AuNP) were spiked to a pilot wastewater treatment plant fed with municipal wastewater for up to 21 days. AuNP were used as chemically less reactive tracer. The uptake of the pristine and transformed NP present in the effluent was assessed using the benthic amphipod Hyalella azteca in fresh- and brackish water exposures at environmentally relevant concentrations of 30 to 500 ng Au/L and 39 to 260 ng Ag/L. The unique isotopic signature of the 109AgNP allowed to detect the material at environmentally relevant concentrations in the presence of a much higher natural Ag background. The results show that the transformations reduce the NP uptake at environmentally relevant exposure concentrations. For 109Ag, lower accumulation factors (AF) were obtained after exposure to transformed NP (250–350) compared to the AF values obtained for pristine 109AgNP (750–840). The reduced AF values observed for H. azteca exposed to effluent from the AuNP-spiked WWTP indicate that biological transformation processes (e.g. eco-corona formation) seem to be involved in addition to chemical transformation.