AbstractSpatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifierNitrosopumilus. In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated withNitrosopumilusnitric oxide nitrite reduction (nirK). The environmental conditions close to organic nitrogen inputs that select for increased transcription inNitrosopumilus(amoCAB,nirK,nirS,nmo,hcp) additionally selected for increased transcription of bacterial nitrite reduction (nxrB) and transcripts associated with anammox (hzo) but not denitrification (bacterialnirS/nirk). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction (nosZ) and changes innosZtranscript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community‐level nitrification–denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaealnirKtranscripts were site‐ and season‐specific. This study indicates that the transcription of archaealnirKin response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling.