Marine systems are becoming increasingly vulnerable to changing climates and human pressures. We show how Models of Intermediate Complexity for Ecosystem assessments (MICE) can be used to better understand ecological connectivity in coastal marine systems under anthropogenic pressures and importantly, quantify impacts from these (often concurrent) pressures. We present examples from three different systems: the Great Barrier Reef (GBR) off tropical north-eastern Australia, the Gulf of Carpentaria (GoC) estuarine-marine system off northern Australia, and a temperate reef in the Southern Benguela upwelling region. We use MICE to assess climate-driven changes that include (1) a lobster-induced regime shift in the Benguela, leading to knock-on effects for other resources and fisheries and (2) impacts on coral reefs that are additionally threatened by Crown-of-Thorns starfish outbreaks along the GBR. (3) Next, we evaluate how anthropogenic disruptions to ecological connectivity, such as via water resource development, impacts key marine habitats and resources in the GoC. Our findings demonstrate the need to consider intricate relationships between species but also their connectivity to the physical environment. We highlight the importance of resource management in buffering ecosystems from pressures beyond the natural processes of coastal marine ecosystems.