As coastal catchment land use intensifies, estuaries receive increased nutrient and sediment loads, resulting in habitats dominated by muddy organic-rich sediments. Nutrient processing and denitrification in estuarine sediments represent important ecosystem functions regenerating nutrients for primary producers, and regulating the ability to remove excess terrestrially derived nitrogen. Denitrification therefore offers resilience to estuaries through mitigating eutrophication. Biodiversity loss and increased mud content are important indicators of estuarine ecosystem degradation, and have been associated with negative effects on soft-sediment ecosystem functioning. However, the impact of these stressors on ecosystem response to nutrient enrichment is unclear. This thesis investigates the response of denitrification to nutrient enrichment with emphasis on the impact of sedimentation stress and biodiversity loss for resilience to eutrophication. To experimentally test soft sediment ecosystem response to enrichment, an effective in situ enrichment method was required. A review of current literature was conducted highlighting a methodological gap, and lack of consistency among published studies. I developed and tested a technique for enriching estuarine sediments using slow release fertiliser. Enrichment effects (pore water ammonium concentrations) scaled with application rate, and greater elevations were observed in deeper (5-7 cm) than surface (0-2 cm) sediments. Enrichment levels were similar to eutrophic estuaries, were maintained for at least seven weeks, and enrichment levels could be partially explained by the sedimentary environment and macrofaunal community. To test the effect of sedimentary environment on denitrification enzyme activity (DEA) response to nutrient perturbation, an in situ enrichment experiment was conducted across an intertidal sedimentary gradient. Findings show that the level of an existing stressor (sediment mud content) can influence ecosystem function response to a second stressor (nutrient enrichment). DEA was supressed by nutrient enrichment, but the effect was greater with more mud content. This study demonstrates that increasing sediment mud content may restrict nutrient processing, facilitating ecosystem shifts toward eutrophication. A field experiment was conducted across a heterogeneous sandflat at selected sites with a gradient in biodiversity to test the effect of macrofaunal community composition on denitrification in response to two levels of nutrient enrichment. Nutrient enrichment caused reductions in DEA as well as functional changes in the macrofaunal community. The degree of suppression of DEA following enrichment was dependent on enrichment level, and was alleviated by a key bioturbating species (medium enrichment), or the abundance and diversity of nutrient processing species (high enrichment). This study provides a prime example of the context dependent role of biodiversity in maintaining ecosystem functioning, underlining that different elements of biodiversity can become important as stress levels increase. To investigate the controls on denitrification at a regional scale (i.e. among estuaries), DEA data and environmental co-variables from five studies across four estuaries was combined and analysed. Mud content accounted for most of the variability in DEA, but other sedimentary and macrofaunal variables were also important. DEA increased with increasing sediment mud content up to a threshold of 30% mud, above which, DEA values were variable but no longer increased. This is significant because mud content is increasing in many estuaries globally, and shows that denitrification can reach a threshold with increasing estuary degradation. The findings of this thesis show that management of nutrients in estuarine ecosystems requires real-world understanding of the context dependent responses of denitrification, and that biodiversity loss and increasing sedimentation may reduce ecological resilience to eutrophication.