Spatial and temporal patterns in benthic diatom assemblage composition and chlorophyll-a production were investigated over a 25 month period within three headwater sub-catchments of the River Eden catchment, NW England. This was undertaken as structural and functional attributes of headwater stream have at large been neglected, despite the long-standing recognition of the importance of interconnectivity of upstream and downstream reaches. Results demonstrated that, catchment specific quasi-seasonal patterns in Shannon-Wiener diversity and in situ fluorometry chlorophyll-a in response to variable discharge-nutrient regimes demonstrating the ability of benthic diatom communities to recover from event-driven disturbances to their underlying equilibrium with water quality. This highlights the stability and resilience of benthic biofilms, in particular their ability to discriminate nutrient pressures between catchments, even in dynamic streams. Investigation of how diatom community attributes (diversity and chlorophyll-a) varied in relation to one another was explored through Shannon-Wiener diversity and in situ fluorometry (ISF) chlorophyll-a revealing a unimodal productivity-diversity relationship. Examination of the critical antecedent period of temporal dynamics in discharge and nutrient conditions (TP and NO3) demonstrated that at-a-point in time community composition is a product of factors, such as phosphorus availability, related to discharge over the preceding 15 - 21 days. Secondly, investigation of patterns in benthic communities at fine spatial scales defined by physical flow biotope units, demonstrated that riffles were more productive than pools but pools displayed greater diversity in benthic diatom composition. Finally, reach-scale temporal dynamics in stream hydraulics and nutrient concentrations and their relation to benthic composition and chlorophyll-a production in riffle biotope units was explored over a 28 day period. This demonstrated a threshold relationship between change in benthic diatom composition and chlorophyll-a with highest diversity and chlorophyll-a observed during sub-scouring rainfall-discharge events preceded by quasi-stable periods in discharge-nutrient condition. Therefore, these investigations of fine-spatial high-temporal patterns in benthic diatom biofilm community structure and ecological functional processes, such as chlorophyll-a production, revealed the time-scale of response and physicochemical sensitivities of benthic ecosystems in headwaters which are important considerations for environmental monitoring and policy decision making.