The combined and interactive effects of multiple stressors threaten coastal ecosystems, yet most ecological risk assessments used to inform environmental management still treat stressors separately. For marine microalgae and seagrass—particularly those common to the Great Barrier Reef, Australia—key stressors include low light from increased turbidity and herbicide exposure that runs off agricultural land. Despite co-occurring in aquatic ecosystems, the effects of these stressors are often studied separately, meaning any combined or interactive effects are overlooked. Here, we aimed to develop a conceptual synthesis of the physiological responses of marine microalgae and seagrass when exposed to these key stressors. We reviewed marine microalgae and seagrass exposure studies to understand how herbicide and light stress is assessed and generated hypotheses for the combined effects. In particular, we predict that photo-physiological, biochemical and whole-organism responses of aquatic plants and algae will interact antagonistically, additively or synergistically depending on the level of light availability and the endpoint measured. We recommend that future multi-stressor exposure experiments study how specific physiological processes interact to impact the growth of important primary producers such as microalgae and seagrasses. This will enable management to accurately determine the ecological risk of multiple stressors to aquatic species and ecosystems.