Understanding eutrophication effects on stream macrophytes is key to meaningful environmental management and governance. However, the response of macrophyte communities to eutrophication is complex and often the effect of eutrophication is obscured by other factors related to habitat variability including flow regime and light availability.In this study macrophyte community composition and abundance was quantified along a eutrophication gradient in 30 lowland streams. Slow flowing, medium sized streams with minimal shading were selected, to focus on examining water quality effects. The internal nutrient status of the plants and the bioavailable nutrient fraction of the sediment was measured and a national database of modelled stream descriptors was used to obtain information about land use and water quality variables. Statistical relationships between macrophyte community composition and clogginess and nutrient, underwater light, and carbon availability and flow disturbance were examined along the eutrophication gradient.Macrophytes with different growth strategies were related to different aspects of eutrophication and non-native taxa were found to dominate eutrophic streams.There was no relationship between nutrient concentrations and nutrient content of the macrophytes but sediment P was correlated with P concentrations in streams.Our results showed that 1) non-native species were common and clogginess was high in unshaded lowland streams with low water clarity and high nutrient and bicarbonate availability; 2) emergent species were associated with high nitrate availability and sediment phosphorus and low disturbance; 3) submerged species prevailed where water column total phosphorus and bicarbonate availability were high; and 4) nutrient concentrations that limit the development of clogginess are expected to be low where bicarbonate is high and flow or other physical disturbance is low. Our findings improve understanding of how stream macrophyte communities respond to changes in water quality related to eutrophication and anthropogenic changes in catchments and will contribute to informed management of macrophytes in streams.