Aim: The factors controlling macrophyte (aquatic plant) composition are complex, recent research showing that the well-studied filtering effects of lake environmental factors are constrained by hydrological and landscape factors. We investigated the factors determining macrophyte composition in lakes over water body and catchment- scales and the transferability of this pattern across lake types. Location: Almost 1000 lakes distributed across Britain. Taxon: Lake macrophytes. Methods: Lakes were partitioned into five types based on subdivision of alkalinity and elevation gradients. Data from botanical surveys were used to compare spatial turnover and nestedness components of beta diversity between lake types. The relative importance of lake environment (based on local physicochemical data), hydrology (e.g. lake and stream density), landscape (e.g. fragmentation indices, land cover) and spatial autocorrelation in explaining macrophyte composition were derived from variance partitioning. Results: Species composition showed strong spatial structuring, suggestive of overland dispersal, enhanced by spatially-correlated abiotic factors such as alkalinity and elevation. Catchment-scale factors (e.g. land use, connectivity) promoted the establishment of different communities (more or less diverse, or differing in composition) but were of secondary importance. Turnover in composition between upland lakes was lower than in other lake types, reflecting a more specialist flora and increased potential for propagule exchange due to spatial aggregation and hydrological connectivity. Main conclusions: Vegetation composition in lakes is more spatially-structured than previously appreciated, consistent with the importance of dispersal limitation, but this does not apply evenly to all lakes, being most acute in lowland high alkalinity lakes. Thus, spatially-structured abiotic factors, such as alkalinity, influence macrophyte composition most (suggestive of niche filtering) in those lakes where human impacts tend to be greatest, although nestedness was also lowest there. By contrast, hydrological connectivity has a proportionally stronger structuring role in upland lakes.