This study focuses on the headwaters of six streams, overlying chalk bedrock in southern England, which were affected by the 1988-1992 drought. The data cover six years, from 1992 to 1997. The clustering method TWINSPAN was used to identify in-channel, macrophyte community groups while geographical information systems (MapInfo, ArcView and Idrisi) were used for analyses of hydrological, geomorphological and land cover data. Changes to macrophyte communities generally, closely reflected changes to river flow regime. However, significant anomalies existed in the dataset, due to other environmental influences. Interactions between local conditions and catchment-wide conditions such as: rainfall, soil moisture deficits, base-flow contributions and channel gradients, played underlying roles in the determination of community types. Communities in catchments with minimal groundwater abstraction took 1-2 years to recover; some in catchments with more intensive abstraction had not recovered 5-6 years after the drought. The indications are that monitoring of macrophyte communities in headwater streams with seasonal flows, may provide useful guidance not just for water resource and habitat management but also in the anticipation of longer term, climatically-driven changes.