Purpose Short-term temporal variability of microphytobenthic primary production is suspected to be of the same magnitude as seasonal variability, but data remain very scarce due to methodological limitations. In this context, a 6-day in situ high-frequency survey was performed in a temperate intertidal mudflat using an automated microprofiling system. Materials and methods In situ microphytobenthic primary production was measured using an automated acquisition system for oxygen microprofiles. More than 900 microprofiles, acquired during six consecutive days in April 2008, allowed the establishment of robust relationships between oxygen production and irradiance. Moreover, simultaneous measurements of fluorescence parameters and oxygen microprofiles during two diurnal emersion periods led to significant correlations between relative electron transport rate (rETR) and gross oxygen production (GOP). Results and discussion The use of an automated system allowed the estimation of oxygen exchanges during both immersion and emersion periods, and to our knowledge, this is the first study presenting continuous measurements during six consecutive days. The intertidal mudflat studied here was characterized by a maximum net oxygen production of 6.74 mmol O-2 m(-2) h(-1). Evidence for microphytobenthic migration behavior was observed during several periods and induced important depletion in oxygen production while irradiance remained high. Consequently, estimations of GOP from fitted photosynthesis-irradiance curves (P-I curves) showed an overestimation of 31 % compared to the GOP actually measured during the whole deployment. Conclusions This study confirmed that oxygen microsensors may be used to record microphytobenthic primary production, as resulting dynamics agreed with fluorescence data, while production values were in accordance with those presented in the literature. High-frequency microprofiles acquisition may be an easy way to monitor short-term temporal changes in microphytobenthic primary production in order to calculate accurate carbon or oxygen budgets for intertidal areas.