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Shallow tidal environments (e.g.bays, estuaries, lagoons) represent one of the most productive ecosystems in the world, and they are threatened by current climate change and increasing human pressure. Monitoring the bio-morphodynamic evolution of these environments is therefore a crucial task that requires a detailed and holistic scrutiny. The present study aims to investigate the temperature of the water-sediment continuum, its effect on the related microphytobenthos (MPB) growth and the related bio-stabilization of the bed sediment surface under different water depth and water turbidity conditions. We investigated the vertical energy transfer and the temperature dynamics by applying a 1-D model to a shallow coastal lagoon. Our results show that the water temperature does not substantially change under different turbidity conditions, whereas the sediment temperature exhibits important changes. Two major factors driving the MPB photosynthetic growth are the sediment surface temperature and the light availability at the sediment bed, which can both be computed using the vertical energy transfer model. We observed that, in general, clear water conditions better promote MPB growth over the entire year. The limiting factor for the photosynthetic process is usually the light availability at the bottom, which increases under clear water conditions. As MPB provides a bio-stabilizing effect on the bed sediments by producing a biofilm on the sediment surface that reduces sediment resuspension, our results suggest a positive feedback between MPB growth and water column turbidity. Furthermore, MPB growth and the related sediment bio-stabilization are clearly affected by the seasonal variation of surface sediment temperature and light availability. This seasonal variation of MPB growth rate and surface sediment bio-stabilization must be considered when studying the long-term morphodynamic evolution of tidal environments. (c) 2018 John Wiley & Sons Ltd.