With the intensification of urban development, agriculture, and forestry, many coastal waters are becoming enriched with nitrogen (N). Long term, excess terrestrial N accumulates in the sediment porewaters impacting benthic fauna and microphytobenthic productivity, altering the complex bio-geophysical interactions that occur on the seafloor. These interactions may influence sediment erodibility and resuspension rates on the seafloor, which have wider ecosystem consequences through changes in water column turbidity, the fluxes of organic matter and sediment porewater nutrients into the water column, and the redistribution of deposited terrestrial materials (i.e. pollutants and sediment). We conducted a field experiment to explore how bio-geophysical interactions change in the context of porewater N enrichment. The experiment enriched plots (4 m2) on an intertidal sand flat in Tauranga Harbour, New Zealand, with three concentrations of N fertiliser (0, 150 and 600 g N m−2; n = 6). After 10 weeks, we collected intact sediments from the plots, and in the laboratory, subjected these sediments to sequential increases in water flow velocity (between 0.05 and 0.4 m s−1) using annular flumes (bed area = 0.17 m−2). We calculated sediment erosion rates and thresholds, measured fluxes of NH4+ and Chlorophyll a across the sediment-water interface and characterised the sediment properties and macrofaunal communities. We anticipated complex feedbacks to occur where porewater N enrichment would increase microphytobenthic biofilm growth, stabilising the sediments (and reducing benthic-pelagic coupling), but at the same time, N enrichment might also alter the macrofaunal community, which graze the microphytobenthos and physically mix the sediment, with a potential destabilising effect (and increase in benthic-pelagic coupling). Although our enriched treatments doubled the biomass of microphytobenthos, altered the macrofauna communities and enhanced the fluxes of Chlorophyll a and NH4+ across the sediment-water interface, sediment erosion thresholds and rates were unaffected. Our results highlight a potential mismatch between the micro- and macro-biotic processes and the larger scale physical forces on dynamic intertidal sandflats, and this mismatch has implications for our ability to scale up small scale processes to entire ecosystems.