The human influence on marine ecosystems is being recognized as a basis for extending the horizons of management. Historical anthropogenic influence has involved a wide variety of factors, including the effects of fishing on the dynamics of individual resource species. More inclusive complexity includes the interactions among species, and their interactions with other aspects of their biotic and physical environment. In this chapter, we review these elements of complexity for the central Baltic Sea. This ecosystem has a long history of human influence and its own special characteristics, due to its geographic location, geomorphic traits, and socio-political context. More and more of the complexity of this ecosystem is being recognized as scientists add to the wealth of documentation regarding the influence of surrounding terrestrial activities, monitor the dynamics of component populations, establish the effects of weather and climate, and illuminate the relationships among the various elements of the ecosystem. There is a great deal of historical information to characterize the changes that have occurred, not only among the various species making up the ecosystem, but also at the ecosystem level. Some of these have involved regime shifts, in part owing to climatic factors. Such significant changes involve more than one of the ecosystem's trophic levels as well as physical features such as salinity, temperature, and oxygen concentration. We begin to understand some of the complexity of ecosystems when we recognize that such factors are not alone, however, and realize that trophic cascade dynamics and feedback loops are also involved.