Effects of metallic nanoparticles (NPs) to the estuarine biota have mostly been shown for concentrations higher than those actually measured or predicted in these environments. To address this gap, a range of concentrations expected to occur in estuarine environments (from 0.01 to 1 µg g-1) was employed in microcosms studies to assess the impact of Cu NPs in the denitrification pathway. That was achieved by quantifying gene expression in estuarine sediments exposed to Cu NPs for up to six days and the potential denitrification rates. Expression of nitrite (nirS) and nitrous oxide (nosZ) reductase genes was enhanced in a timewise manner upon exposure to Cu NPs < 50 nm. For Cu NPs 1 µg g-1 an increase in gene expression could be seen immediately after 1 h of exposure, and continuing to be enhanced up until 7 h. For Cu NPs 0.01 µg g-1 an increase in gene expression could only be seen after 4 h or 7 h of exposure; however it continued to rise up until 24 h. Concomitantly to increased gene expression the potential denitrification rate was increased by 30 %. In any case, after 48 h the expression levels were no longer different from the non-exposed control. For the exposure to Cu NPs < 150 nm no change in gene expression could be seen. Our results suggest that deposition and adsorption of Cu NPs < 50 nm to estuarine sediments promotes the immediate and transient expression of key genes of the denitrification pathway. The long term impact of continuous inputs of Cu NPs into estuaries deserves renewed analysis to account for their effects, not just on the biota, but especially on ecosystems services.