Ecological functions in estuarine seagrass and unvegetated soft sediment habitats underpin many valuable ecosystem services. However, changing land-use and climate are accelerating inputs of fine terrestrial sediments, threatening these habitats. The prolonged suspension of fine sediments can reduce seafloor light availability and long-term accumulations increase sediment mud content (particles < 63 µm), both of which could have significant consequences on ecosystem functioning. Understanding how ecosystem functioning may respond to environmental change is vital to estuary management. In this thesis, I investigated the short- and long-term effects of elevated terrestrial sediment inputs on benthic primary production and nutrient cycling in intertidal seagrass meadows (Zostera muelleri) and microphytobenthos-dominated unvegetated habitats. To investigate the effects of reduced seafloor light availability and prolonged submergence periods resulting from global heating induced sea-level rise, I conducted a two-year seasonal in situ assessment of photosynthesis-irradiance relationships during submerged and emerged conditions in an adjacent seagrass meadow and unvegetated sandflat. Submerged gross primary production (GPP) in both habitats and emerged GPP in the seagrass habitat were strongly controlled by light availability. Higher rates of light-saturated GPP were found during submerged periods compared to emerged periods in both habitats, but this difference was most pronounced in the unvegetated habitat. If the water-column remains clear, sea-level rise could therefore increase daily GPP in soft sediment habitats. However, declines in submerged GPP with increased water-column turbidity will be exacerbated with sea-level rise. Across a natural mud content gradient, I measured primary production in seagrass and unvegetated habitats to address the long-term implications of elevated sediment inputs. In sediments with ≤ 35 % mud content, net primary production (NPP) and GPP was independent of mud content in both habitats. However, extending the mud gradient in unvegetated habitats to 49 % (seagrass habitats restricted to ≤ 35 % mud content) resulted in NPP and GPP declining with increasing mud content. These results highlight that loss of seagrass meadows resulting in expansion of unvegetated habitats could lead to reductions in intertidal production; seen most acutely in areas with high mud content (≥ 39 %). I also investigated the spatial and temporal variability in nutrient cycling in seagrass and unvegetated habitats to examine how environmental gradients affected sediment nutrient fluxes and denitrification rates. Ammonium effluxes were lower in the seagrass compared to the unvegetated habitats and were lower in both habitats during light compared to dark conditions. Denitrification rates were similar in both habitats but were found to decrease with increasing mud content. Overall, denitrification efficiency was highest in the seagrass habitat. These results indicate that future seagrass decline and/or increased mud content in soft sediment habitats will reduce resilience to eutrophication. This thesis demonstrates that future seagrass decline and elevated terrestrial sediment inputs are likely to have serious implications on the high rates of primary production and nutrient cycling of intertidal seagrass meadows and unvegetated habitats. Furthermore, it highlights the value of measuring ecosystem functions in different soft sediment habitat types across multiple spatial and temporal scales to inform future management against anthropogenic stressors.