Estuarine intertidal flats are hot spots of benthic primary production. However, globally these ecosystems are threatened by rising sea-level and accelerated inputs of terrestrial sediments which alter seafloor light availability. Despite its importance, there is minimal in situ data detailing how changing light availability affects production in seagrass meadows and on microphytobenthos dominated sandflats. To rectify this, in a seagrass meadow (Zostera muelleri) and an adjacent sandflat habitat we derived in situ seasonal photosynthesis-irradiance (P-I) curves for two years during submerged and emerged periods. P-I curves demonstrated strong light responses in both habitats during submergence, but during emergence in the unvegetated sandflat there was little relationship between light availability and photosynthesis. Seagrass habitats were also more productive than the unvegetated sandflat during both tidal states and both habitats showed reduced production during emergence. Integrating our seasonally derived P-I curves during submerged and emerged conditions into a conceptual model suggests that increasing submergence time could increase annual gross primary production in both habitats provided the water column remained clear. However, reductions in water clarity will decrease submerged primary production increasing the reliance on emerged production which will be diminished with sea-level rise. Regional management of water clarity may therefore be key to providing resilience to intertidal habitats against the inevitable effects of sea-level rise.