Large rivers can retain a substantial amount of nitrogen (N), particularly in submerged aquatic vegetation (SAV) meadows that may act as disproportionate control points for N retention in rivers. However, the temporal variation of N retention remains unknown since past measurements were snapshots in time. Using high frequency measurements over the summers 2012-2017, we investigated how climate variation influenced N retention in a SAV meadow at the confluence zone of two agricultural tributaries entering the St. Lawrence River. Distinctive combinations of water temperature and level were recorded between years, ranging from extreme hot-low (2012) and cold-high (2017) summers (2 ˚C and 1.4 m interannual range). Using an indicator of SAV biomass, we found that these extreme hot-low and cold-high years had reduced biomass compared to hot summers with intermediate levels. In addition, change in main stem water levels were asynchronous with the tributary discharges that controlled NO3- inputs at the confluence. We estimated daily N uptake rates from a moored NO3- sensor, and partitioned these into assimilatory and dissimilatory pathways. Measured rates were variable but among the highest reported in rivers (median 576 mg N m-2 d-1;, range 60 – 3893 mg N m-2 d-1) and SAV biomass promoted greater proportional retention and permanent N loss through denitrification. We estimated that the SAV meadow could retain up to 0.8 kt N per year and 87% of N inputs, but this valuable ecosystem service is contingent on how climate variations modulate both N loads and SAV biomass.