Soft sediment intertidal habitats provide valuable ecosystem services to millions of people worldwide yet are under intense anthropogenic pressure. In particular, the intensification of land derived sediment and nutrient delivery has resulted in elevated water column turbidity and nutrient over-enrichment, both of which can diminish ecosystem functionality. Identifying how these stressors interact and influence benthic ecosystems is crucial to understanding the resilience of these valuable habitats and to help manage effectively to prevent shifts towards ecological tipping points. This thesis therefore investigates the response of benthic primary production and biogeochemical cycling to two pervasive stressors; increasing water column turbidity and sediment nutrient enrichment. Water column turbidity directly restricts the availability of light to microphytobenthos (MPB), a key primary producer in soft sediment intertidal habitats. However, the degree to which turbidity may limit primary production across New Zealand was largely unknown. I recorded light availability at the seafloor over a 9-month period at 22 sites situated within 14 estuaries. Coupled with a global literature compilation of photosynthesis-irradiance curves, the proportion of time MPB were light limited during submergence ranged from a median of 55–100 %. For estuaries close to 100 % light limitation, emerged intertidal areas represent a refuge for MPB production which is vulnerable to sea-level rise. Using hypsometric curves, the intertidal area of my study estuaries was predicted to decrease by 27–94 % under a 1.4 m rise in sea-level. The combination of high light limitation during submergence and large losses of intertidal area will increase vulnerability to the loss of MPB production and the associated ecosystem services, which can push these ecosystems towards tipping points. Anthropogenic stressors often occur concomitantly, and therefore understanding how differing degrees of water column turbidity may interact with other stressors, such as increasing nutrient enrichment and influence benthic productivity over alternating periods of submergence and emergence were investigated. A field manipulation study was designed to enrich porewaters at three levels for 20 months, at six sites that spanned a gradient in water column turbidity. While nutrient enrichment had no detectable effect on MPB primary production, water column turbidity had a significant influence, explaining up to 40 % of the variability during tidal submergence, followed by temperature and sediment characteristics. In addition, negative net primary production (NPP) and therefore net heterotrophy for the most turbid estuaries during tidal submergence resulted in an increased reliance on production during emerged periods. This study highlights the prominent role of turbidity over porewater nutrient enrichment in moderating MPB production and supports earlier conclusions of the increasing importance of emerged periods to maintain the health and functioning of coastal habitats. Soft sediment intertidal habitats are not only hot spots for benthic productivity, but they also play a fundamental role in biogeochemical cycling. The influence of increased nutrient availability on nitrogen and carbon cycling was investigated after 15 and 20 months of nitrogen enrichment. This study highlighted the limited capacity for denitrification, a key process in removing bioavailable nitrogen, to mitigate large increases in nitrogen availability, as evidenced through the consistent rates of net denitrification and reductions in the efficiency at which nitrogen was removed. Denitrification rate was most strongly correlated to carbon supply, trophic status and to a lesser extent, macrofaunal diversity. In addition, analysis of factor-ceiling relationships revealed the vulnerability of estuaries to increasing stressor loads. The appearance of significant nonlinearities with increasing nitrogen enrichment suggests alterations to the interactions of intrinsic dynamics and drivers which can fundamentally alter biogeochemical cycling within soft sediments and increase the likelihood of abrupt non-linear shifts. Overall, the findings of my thesis demonstrate how the health and functioning of coastal ecosystems can be significantly diminished under increasing anthropogenic stress, and that the vulnerability of coastal ecosystems to the loss of ecosystem functionality will change in the future as global scale stressors intensify.