A unifying observation in ecology is that environmental context can play a key role in regulating the sign, strength, and mechanisms of species interactions. Estuaries and coastal seas are ideal ecosystems for exploring the impacts of environmental variability on ecological interactions because they are characterized by strong, dynamic gradients of abiotic conditions, such as physical disturbance and biogeochemical stress. Estuaries also are heavily impacted by biotic disruptions, including overexploitation of top predators and invasion by non-native species. For my dissertation, I explored the effects of abiotic and biotic environmental context on species interactions in subtidal and intertidal meadows of eelgrass Zostera marina, a marine angiosperm and key habitat-forming species in temperate estuaries worldwide, in three unique chapters. First, I tested how disturbance mediates competition between eelgrass and the burrowing ghost shrimp Neotrypaea californiensis in several California estuaries by conducting a series of transplantation and disturbance experiments. I found that both live eelgrass and structural mimics of belowground eelgrass tissues cause rapid declines in local ghost shrimp abundances, indicating that plant structure is an important mechanism in determining ghost shrimp distributions. However, ghost shrimp quickly colonize disturbances to eelgrass patch edges, which are common in shallow estuaries. Thus, coexistence is maintained by disturbance and a competition-colonization trade-off: eelgrass is competitively superior, but physical disturbances permit ghost shrimp coexistence at the landscape scale by modulating the availability of space. Second, I explored how light availability influences the sign, strength, and mechanisms of interactions between eelgrass and blue mussels, Mytilus edulis. I hypothesized that light availability regulates bivalve habitat modification and subsequent impacts on seagrasses by shifting net effects between alleviation of nutrient stress and intensification of sulfide stress. I manipulated light availability and blue mussel abundance in eelgrass mesocosms and measured biogeochemical and plant responses. I found that light modifies the effect of mussels on porewater ammonium, but eelgrass was not nutrient limited and, therefore, mussels did not enhance growth. Mussels increase sediment sulfides irrespective of light availability and, by reducing net oxygen flux (production and respiration), mussels and low light availability exacerbate sulfide intrusion of eelgrass tissues. Surprisingly, I found that sulfide stress did not affect plant growth, survival, or energy stores. Thus, habitat modification by mussels represents a risk to eelgrass, especially during low productivity conditions, but eelgrass can resist harm from short-term stress, even during light limitation. These findings suggest that while bivalve impacts on seagrasses may be variable in oligotrophic estuaries, they are likely negative in eutrophic systems, which are increasing globally. Third, I examined how invasive mussels impact their native bivalve competitors through both direct effects and indirect, predator-mediated interactions. Competition is a major process by which introduced species impact native populations, communities, and ecosystems, but ecological theory predicts that invading prey can also interact with their native competitors indirectly through shared native predators. Nevertheless, indirect effects are largely overlooked in invasive species science and management. In southern California estuaries, introduction of the Asian mussel Arcuatula senhousia has been linked to profound changes in native bivalve assemblages. I performed three field experiments to assess the mechanisms of competition between Arcuatula and native bivalves, and evaluate the potential for Arcuatula to indirectly mediate native predator-prey dynamics. I found that Arcuatula reduces the diversity, abundance, and size of native bivalve recruits by preemptively exploiting sediment surface space. When paired with native shallow-dwelling clams, Arcuatula reduces adult survival through overgrowth competition. However, Arcuatula also attracts native predators, indirectly increasing predation of native clams, especially poorly-defended species. Therefore, the vulnerability of invasive prey to predation can greatly exacerbate impacts on their native competitors. Overall, my dissertation improves our basic understanding of the causes and consequences of variation in species interactions in shallow estuaries and coastal lagoons. Furthermore, this research enhances our ability to predict the impacts on species interactions caused by human-induced ecosystem disruptions, such as habitat destruction, eutrophication, and non-native species introductions, which are widespread concerns for estuaries and coastal seas.