Soft-sediment coastal ecosystems are important sites for a multitude of ecosystem functions, including primary production, organic matter recycling and nutrient processing. Intertidal areas host an array of fauna and flora that can alter pathways and processes which underpin function, support higher food webs and ecosystem services. Anthropogenic impacts on coastal areas are increasing in frequency and intensity. One of the key pressures to New Zealand estuaries, and globally, is that of increased run-off from land. This can cause eutrophication, which is the ecological response to increased nutrients. Waihī Estuary, in Bay of Plenty, New Zealand, has been influenced by farming intensity, coastal development, and stream channelising, which has increased sediment and nutrient inputs recently and over the past 90 years; resulting in frequent algal blooms. This thesis explores the effect eutrophication is having on ecosystem functioning along a gradient of change. Field sampling was carried out over summer 2018 and used space as a proxy for time, sampling seven sites over a naturally occurring eutrophication gradient. Solute exchanges (O₂, NH₄⁺-N, PO₄ᶟ⁻-P, NOₓ-N), were measured using benthic flux chambers over one tidal period. At each site, environmental variables and the macrofaunal community were also quantified. Biotic and abiotic drivers of function were examined firstly on a site by site basis, to gain resolution of fine scale flux dynamics. Non-metric distance based linear models were then created to evaluate changes in function across the spectrum of sites using sequential tests where organic matter content was fitted first. Results from this study indicate increasing organic matter content was a major contributing factor to ecological shifts, cascading biotic and abiotic interactions, and feedback loops. Increasing organic matter content increased sediment oxygen demand to the point of hypoxia (and potentially anoxia), particularly where algal mats (Gracilaria spp.) were present. Gracilaria spp. seemingly capped the sediment, prevented light penetration and significantly influenced sediment oxygen consumption. Photosynthetic efficiency (GPP𝒸ₕₗ ₐ) also decreased with organic matter enrichment. In association with increased sediment oxygen consumption, NH₄⁺-N and PO₄ᶟ⁻-P showed a 2.6 and 2-fold increase in efflux (respectively) under dark conditions. Redox pathways were altered as eutrophication increased and, ii where oxygen was depleted, NOₓ-N was taken up by sediments and utilised as an electron acceptor. Organisms responded positively to organic enrichment to a point, but once this threshold was exceeded, taxonomic richness and individual abundance reduced. Although sediment variables explained the greatest proportion of variance in flux models across the gradient, key bioturbating species had disproportionate effects on solute exchanges. These organisms were sensitive to changes in sediment conditions. The New Zealand cockle Austrovenus stutchburyi and tellinid bivalve Macomona liliana were the first species to decline in response to eutrophication. A. stutchburyi increased NH₄⁺-N efflux, but declined in number with eutrophication, which simultaneously increased NH₄⁺-N efflux. A burrow building polychaete, Ceratonereis spp. enhanced NOₓ-N uptake to sediments indicating nitrificationdenitrification coupling. However the opportunistic amphipod Paracorophium spp. dominated site 4, where increased NOₓ-N efflux (though continuous burrow ventilation) indicated a potentially important species for ammonification and subsequent nitrification. This study demonstrates how changes in ecosystem functioning due to eutrophication can result in undesirable shifts within estuarine systems. These changes are often difficult to remediate and can impede the services that estuaries provide.