Headwater streams are an important feature of the landscape, with their diversity in structure and associated ecological function providing a potential natural buffer against downstream nutrient export. Phytobenthic communities, dominated in many headwaters by diatoms, must respond to physical and chemical parameters that can vary in magnitude within hours, whereas the ecological regeneration times are much longer. How diatom communities develop in the fluctuating, dynamic environments characteristic of headwaters is poorly understood. Deployment of near-continuous monitoring technology in subcatchments of the River Eden, NW England, provides the opportunity for measurement of temporal variability in stream discharge and nutrient resource supply to benthic communities, as represented by monthly diatom samples collected over two years. Our data suggest that the diatom communities and the derived Trophic Diatom Index, best reflect stream discharge conditions over the preceding 18–21 days and Total Phosphorus concentrations over a wider antecedent window of 7–21 days. This is one of the first quantitative assessments of long-term diatom community development in response to continuously measured stream nutrient concentration and discharge fluctuations. The data reveal the sensitivity of these headwater communities to mean conditions prior to sampling, with flow as the dominant variable. With sufficient understanding of the role of antecedent conditions, these methods can be used to inform interpretation of monitoring data, including those collected under the European Water Framework Directive and related mitigation efforts.