Exposure of contaminants in coastal areas has been on the rise with increasing urbanization of natural environments. These contaminants are known to effect organisms in multiple ways, such as directly increasing mortality, or indirectly altering many of their behaviors, such as sensing predators and foraging. Since seagrass habitats are heavily influenced by anthropogenic factors, organisms found in these ecosystems often experience constant exposure to non-degradable contaminants such as heavy metals. Eelgrass (Zostera marina) persistence is promoted by mesograzers (small crustaceans and gastropods) that control competing epiphytic algae growing on seagrass blades. Along with nutrient levels, this top-down control of a dominant competitor (algae) plays a substantial role in dictating eelgrass health, particularly at high levels of eelgrass structural complexity. However, mesograzers can be negatively affected by contaminants at high levels. I conducted a manipulative field experiment on epifaunal colonization of eelgrass in San Diego Bay, and a companion lab experiment on epifaunal grazing, to determine how epiphytic algae, the mesograzer community, and rates of herbivory are interactively affected by dissolved copper and habitat structural complexity. In the field, copper spiked plaster blocks and artificial seagrass units were used to create realistic pulse events of contamination for two levels of habitat structural complexity. I found that the abundance of epiphytic algae decreased with increasing copper, but that copper had no effect on epifaunal abundance or diversity, which responded strongly only to habitat structural complexity. In the lab experiment, I found complex interactive effects of copper concentration and habitat complexity on grass shrimp grazing rates. Low elevated levels of copper resulted in higher grazing in low complexity vs. high complexity eelgrass, in contrast to trends in ambient and high levels of copper as well as in previous experiments. In both low and high structural complexity eelgrass, grass shrimp grazing impact was highest when copper was elevated compared to ambient levels. In order to set effective regulations, understanding both the direct and indirect interactions between organisms and their environment is key in conserving and managing eelgrass habitat.