In-stream macrophyte growth was extensive, with maximum percentage cover of 80 % recorded in September and October 2003. The macrophyte cover significantly altered flow patterns and flow velocities within and between the macrophyte stands. The reduced flow velocities within the plants promoted sediment trapping, reaching volumes of 0.085 m3 of fine sediment trapped per metre square of vegetation at one site. The effective particle sizes of the sediments trapped within Ranunculus stands were dominated by the 250–500 μm fraction from March to July 2003 whereas a higher proportion of smaller fractions occurred from October to December. Faecal pellets were highly abundant in the sediments trapped within Ranunculus stands (up to 2.2 × 108 faecal pellets per m2) and their dimensions (total size range 25–400 μm) fall within the dominant size fraction of the trapped sediments. Our findings demonstrate the need to consider the biogenic component of the fine sediments in chalk streams in future studies of sediment and nutrient dynamics.