Spatial variation in the distribution and abundance of submerse macrophytes in the Mary River, a subtropical Australian river, was examined at 29 sites on four occasions (116 samples) over a 1 year period. Thirteen submersed macrophyte taxa representing seven families were recorded during the study period. Submersed macrophyte cover was generally patchy and mean quadrat cover per sample was below 7% for every recorded taxon. Classification and ordination identified four distinct groups characterised by differences in submersed macrophyte abundance and associated environmental variables. Three of the four groups were characterised by different abundances of three core taxa, Myriophyllum verrucosum, Vallisneria nana and Potamogeton crispus. The distribution of the four sample groups within the Mary River catchment was associated with two environmental gradients, the first gradient representing discharge intensity, discharge variability and total Kjeldahl nitrogen (TKN) concentration and the second gradient representing discharge intensity, substrate composition, riparian canopy cover and total phosphorus (TP) concentration. Both environmental gradients were constrained by geomorphology at the catchment as well as the reach scale. Our findings are consistent with a general conceptual model that highlights the importance of major environmental gradients in structuring submersed macrophyte assemblages. Yes Yes