Anthropogenic climate change is causing sea level rise and extreme weather events, which act as stressors on soft sediment ecosystems. Soft sediments are ubiquitous along coastlines and carry out important ecosystem functions such as nutrient recycling and primary production. Ecosystem functions are underpinned by multiple ecosystem components, which include community composition and environmental characteristics, creating an ecosystem function network. To understand how climate change affects the number and strength of connections within ecosystem function networks, we simulated sea level rise and storm derived terrigenous sediment deposition on an intertidal soft sediment flat in Aotearoa New Zealand. We collected samples to build an ecosystem network for each treatment: sea level rise, sediment deposition, and sea level rise + sediment deposition. We found that all treatments caused network simplification with respect to the number and strength of connections from ecosystem components to functions. Sea level rise caused more severe simplification than sediment deposition, and combined sea level rise and sediment deposition caused marginally higher network simplification compared to sea level rise alone. These findings indicate the more subtle changes that can occur within an ecosystem under climate change stress, highlighting the importance of considering ecosystem responses as a whole.