Southcote is bordered to the south by the Holy Brook and the River Kennet; as such much of the land in the south of the area is floodplain. The proximity of Southcote to the river has led to flooding of roads and residences, particularly during the 2013–2014 United Kingdom winter floods. Flooding is exacerbated by the routes of the Holy Brook and railway line; the railway crosses the stream by bridges and culverts and in some locations the embankment acts as a bund, inhibiting the dissipation of floodwater. Similarly, a report by West Berkshire Council found that during the 2013–14 floods the single track road between the Holy Brook and the Kennet at Southcote Mill "acted as a barrier until the rising waters backing up in the flood plain fields finally breached".