The objective of our modeling was to better understand the relationship between seagrass and water-column and sediment stressors (i.e., light, organic and particle sedimentation, sediment nutrients and sulfides). The model was developed and optimized for sediments in Thalassia testudinum seagrass beds of Lower Laguna Madre, Texas, USA and is composed of a plant sub-model and a sediment diagenetic sub-model. Simulations were developed for a natural stressor (harmful algal bloom) and an anthropogenic stressor (dredging event). The harmful algal bloom (HAB) was of limited duration and the simulations showed no effect of the algal bloom on biomass trends but did suggest that sediment sulfides could inhibit growth in the bloom duration and intensity were greater. The dredging event resulted in sedimentation of a layer of organically rich material and reduction of canopy light for a period of months. The simulations suggested that the seagrass could have recovered from the effects of light but residual effects of high sulfides in the sediments would make the region uninhabitable for seagrasses for up to 2.5 years. These modeling exercises point out the importance of using a geochemical model to evaluate the impact of reduced light and enhanced organic loading from both natural and anthropogenic stressors to seagrass.