In estuaries, sediment properties dominate the inhabiting flora and fauna and their role in energy flows and nutrient cycling. Whilst sediment transport is a natural, key process, human intervention in estuaries and their catchments has altered the regime of terrigenous sediment loading and pose both short and long-term consequences to ecosystem functioning. Temporary increases in turbidity reduce light availability for primary production by microphytobenthos (MPB) that fuel benthic communities. Long-term alteration of grain size properties changes the distribution of key macrofaunal species and how they interact with their environment, carrying potentially serious implications for the ecological functioning of these systems. Our knowledge of how benthic ecosystems respond to changes in sedimentary regimes is crucial to our ability to project and manage the impacts of environmental change. In this thesis, I investigated the multifaceted effects of increased sediment loading on the benthic biota and their functioning using natural and experimental sedimentary gradients. An in situ experiment was conducted on an intertidal sandflat to examine the effects of short-term increases in suspended sediment concentration (SSC) on benthic autotrophic (primary production) and heterotrophic processes. In sunlit conditions, increases in SSC led to dramatic declines in net primary production and concomitant increases in NH₄⁺ efflux from the sediment to the water column. Although sediment chlorophyll-⍺ concentration increased with higher levels of SSC, a result that was likely a photoadaptive response to reduced light intensity, SSC reduced O₂ production per unit of chlorophyll -⍺ . SSC had no significant effect on sediment properties or heterotrophic processes such as sediment oxygen consumption or nutrient efflux, suggesting that temporary increases in suspended sediments (within the range of SSC tested) primarily affected photosynthetic processes. Sediment properties, macrofaunal diversity and biogeochemical fluxes were measured across natural gradients of silt and clay (hereafter mud) to determine the effects of habitat change associated with chronic sediment loading on the structure and functioning of benthic communities. There were significant declines in measures of macrofaunal diversity and the maximum densities of key bioturbating bivalves (Austrovenus stutchburyi and Macomona liliana) with increased mud content. Concurrently, the maximum rates of sediment oxygen consumption (SOC), NH₄⁺ efflux (a proxy of nutrient regeneration)and biomass standardised gross primary production (GPPChl-⍺) also decreased with increasing mud content. A. stutchburyi contributed disproportionately to variation in SOC and NH₄⁺ efflux, suggesting that losses of strongly interacting key species concomitant with increased sediment mud content could have a significant impact on ecosystem function. The results from this study demonstrate the significant loss of ecosystem function in intertidal sandflats that is likely from increased sediment mud content associated with long-term increases in sedimentation stress. The spatial distributions of MPB biomass, macrofaunal grazer abundances and deposit feeding activity were measured across a gradient of sediment mud content to determine relationships between grazers and MPB biomass across transitional sedimentary environments. The density of feeding traces produced by M. Liliana was measured as a proxy of deposit feeding activity by this species. MPB biomass was generally lower in areas with higher deposit feeding activity but this relationship was scale dependent, emerging over larger areas (tens of centimetres) but absent at local (centimetre) scales relative to the animal’s feeding ambit. Despite higher MPB biomass in muddy sediments, feeding trace density was markedly lower, suggesting lower feeding activity and trophic exchange in muddy compared with sandy sediments. The suspension feeding bivalve A. stutchburyi was positively associated with MPB biomass and the interaction between A. stutchburyi density and mud was the strongest predictor of MPB biomass. Thus, non-trophic interactions that potentially facilitate production may override the deleterious effects of grazing on MPB biomass by large macrofaunal species. This thesis demonstrates the high capacity of sandflat systems for primary, secondary production and nutrient regeneration and the degradation of these ecological properties and functions in muddier and more turbid systems. The decline in this functional capacity reflects the alterations of multiple ecological components and their interactions corresponding to habitat change. Defining changes in these interaction networks can improve our ability to track changes in ecosystem functioning and elucidate underlying pathways and potential mechanisms. In particular, this thesis highlights the value of observing changes in these ecological properties and functions across natural and experimental gradients at the appropriate scales in time and space over which stressors operate.