Intertidal habitats provide a wealth of ecosystem services including fuelling oceanic food webs and processing nutrients however, understanding the response of these habitats to emersion has been largely overlooked. Increasing rates of terrestrial sediment reaching the coast is degrading the water column light climate and thus the productive capacity of benthic primary producers during immersion. As a result, low tide production may become more significant in the near future. There is currently little knowledge regarding how primary production changes over an emersion period, in particular how it varies with habitat type and the impacts of environmental stressors, such as desiccation. This study explored the spatial (between habitats) and temporal (over austral summer and over individual emersion periods) variability in benthic primary production within a temperate barrier-enclosed estuary. Research was conducted in three intertidal habitats (encompassing differences in sediment properties, dominant primary producers, and macrofaunal communities) in Tauranga Harbour, New Zealand. Seagrass (Zostera muelleri), shellfish, and polychaete dominated habitats were chosen as they represent common intertidal habitats found in temperate regions. Emerged gross primary production (GPP), at the community scale, was quantified by measuring changes in carbon dioxide (CO2) concentration over time during a series of successive three minute incubations spanning the entirety of the low tide period. This was achieved by measuring fluxes of CO2 in benthic incubation chambers under both light and dark conditions, to derive net primary production (NPP) and sediment oxygen consumption (SOC) respectively. CO2 fluxes were then analysed to determine whether sampling month or time exposed had a significant difference on the photosynthetic capacity of different intertidal habitats. Sedimentary and environmental variables were sampled to identify any key predictors of emerged primary production. Primary production (both NPP and GPP) measured in the seagrass habitat exceeded both bare sediment habitats (by up to 11 times) due to inherent differences in the dominant primary producers (seagrass vs. microphytobenthos) and the associated photosynthetic biomass. Within bare sediment habitats, significant differences in primary production were attributed to variation in sedimentary characteristics (particularly mud content) and macrofaunal communities. GPP was standardised for photosynthesising biomass to provide a measure of photosynthetic efficiency (GPPSG and GPPchl a). Once standardised, month to month differences within individual habitats disappeared, thus initial temporal differences measured over austral summer were primarily attributed to differences in biomass. Temporal trends over individual emersion periods were not consistent across all habitats. GPPSG in the seagrass habitat increased hourly (from T1 to T4) on multiple sampling occasions, while no consistent trends were evident in either of the bare sediment habitats. This study recognises that emerged primary production can equal, if not exceed, rates of production and carbon fixation during immersion. This reinforces the importance of including emerged intertidal habitats in global carbon budgets. Especially as the contribution of low tide production will become increasingly important as elevated turbidity levels may compromise the productive capacity of submerged habitats. Understanding the dynamics of intertidal habitats under emersion is valuable as they represent a significant proportion of coastal ecosystems in New Zealand and around the globe.