Estuarine ecosystems are important zones for primary productivity and nutrient processing, have rich communities of plants and animals and support important fisheries and are fundamental to food webs. Intertidal habitats in estuaries are highly dynamic environments, subject to tidal variation and often have strong environmental gradients of salinity, turbidity and bed sediment grain size. These environmental factors contribute to the diversity of macrofaunal assemblages which vary over a range of spatial and temporal scales. This study was based in the Manukau Harbour, New Zealand, and aimed to investigate the spatial variation of nutrient processing within the harbour, and whether this variation is best explained by biotic or abiotic variables. Additionally, DistLM models were employed to find if either macrofauna functional groups or key species in these groups serve as better predictors of ecosystem function. To provide empirical information to a project designing a whole-estuary nutrient mixing model, a team of ecologists deployed benthic incubation chambers (0.25 m2) to measure solute fluxes, and assessed the macrofauna community and sediment characteristics at 6 intertidal sandflat sites in the Manukau Harbour over a 4 day period in December 2016. Denitrification rates were measured at 2 sites to provide information on nitrogen removal from the harbour. This thesis deals specifically with how the macrofaunal communities and how they relate to and influence nutrient fluxes. Macrofauna collected from the Manukau Harbour were assigned functional groups based on species specific traits. Multiple regression models were performed using functional groups and ecosystem variables as predictors, and dark chamber fluxes of O2, NH4+ and NOx- as response variables. Significantly correlated functional groups (p < 0.05) were substituted for their constituent species to determine whether functional groups or individual species served as better predictors of ecosystem functioning. The results indicated that while functional groups may provide redundancy in terms of multiple species carrying out similar functional roles, there are key species that dominate these roles. In addition to the macrofauna functional groups, several environmental variables (mud content, phaeophytin biomass and organic content) served as important predictors for changes in ecosystem functioning. This suggests that macrofauna functional groups form complex relationships with environmental variables which influence ecosystem functioning through benthic metabolism and excretion and macrofaunally-mediated such as bioturbation and irrigation of sediments. These biological processes alter the oxic-anoxic boundaries and facilitate the breakdown and remineralisation of deposited organic matter, fuelling primary productivity and nitrogen cycling. At two sites where denitrification was measured, the total amount of nitrogen leaving the water column was similar (242.3 and 234.8 µmol N m-2 h-1), however the rates of denitrification of these sites was significantly (p = 0.0001) different, suggesting that permanent removal of nitrogen varies spatially across the harbour, which can have important connotations for ecosystem management.