Estuaries are highly dynamic systems with strong physical and biological gradients which drive ecosystem functions. Increasing anthropogenic pressures within these ecosystems has led to a marked decline in global estuarine health by altering key ecosystem functions such as carbon consumption. Current research primarily focuses on individual stressors, overlooking potential interactions among multiple stressors. This study aims to investigate individual and interacting effects of two anthropogenically derived pressures, namely microplastics, and nitrogen loading, across three soft-sediment habitats with contrasting infaunal communities. Habitats were chosen based on dominant functional traits within the community: top-down deposit-feeding worms, deep-dwelling facultative-feeding clams or a mix of both. In-situ organic matter assays, each containing different stressor combinations (nitrogen addition, microplastics, combined stressors, controls), were used to assess whole-community carbon consumption—an indicator of ecosystem functioning. Our results highlight how benthic community structure is a key factor that moderates carbon cycling in sediments in response to multiple stressors. Carbon consumption rates varied greatly across stressor treatments, depths and the dominant functional trait indicating non-linear interactive effects. By understanding these complex interactions, our study contributes to a deeper understanding of estuarine ecosystem dynamics, and in particular, potential implications of anthropogenic pressures on carbon burial and processing.