The dataset contains results from surveys recording the cover and area of aquatic macrophytes at four transects on the River Lambourn, collected monthly between March 11 2009 and September 30 2014. The River Lambourn is a tributary of the River Thames, the principal river in the south-east of England. The CEH River Lambourn Observatory comprises a 600 m reach of river and 24 acres of associated water meadows at Boxford, Berkshire. The surveys were designed to provide an estimate of the area and cover of the three most common aquatic macrophytes and an estimate of the area of the wetted channel at four transects. The species recorded were Ranunculus penicillatus ssp. pseudofluitans (with Ranunculus penicillatus ssp. pseudofluitans x Ranunculus peltatus hybrid also present), Callitriche platycarpa (with some Callitriche obtusanglia) and Berula erecta. The four transects were selected in order to represent a combination of shallow/fast flowing areas and deeper/slower flowing areas, as well as shaded and unshaded reaches. Full details about this dataset can be found at https://doi.org/10.5285/37f0ab37-78f1-4ca6-b51f-950e43977b16