Abstract. Here we report a time series of experiments performed in a microcosm to test the response of hypersaline microbial mats to diverse atmospheric CO₂ conditions. Different from most part of the literature, our study used a sample chamber were carbon dioxide concentration was controlled. Our aim was to test the effect of different atmospheric CO₂ conditions in benthic gross and net primary production, and respiration. This study showed for the first time to our knowledge absolute carbon limitation in a microbial mat. Oxygen concentration profile varied from a flattened shape to almost linear when atmospheric CO₂ at the chamber reached 0 ppm, with NPP reaching 0 nmol cm⁻³ s⁻¹ throughout most part of the profile. In this conditions sediment community respiration represented 100% of GPP. Extreme close coupling between primary production and respiration in microbial mats can be even self-sustainable in environments with temporally no atmospheric CO₂ available. When submitted to even high CO₂ concentrations (550 ppm), our sample showed a characteristic shape that indicate limitation composed by a more rectilinear oxygen profile, and NPP peaks mainly restricted to deeper layers. Therefore, we suggest that phototrophic communities in aquatic shallow ecosystems can be carbon limited. This limitation could be common especially in ecosystems submitted to variable water depth conditions, like coastal lagoons and intertidal sediments.