Abstract: Global biodiversity has been decreasing globally and at times at an unprecedented rate. The alarming loss of keystone species can at times outpace research documenting their effects on their ecosystems. Making the link between benthic communities and ecosystem functions requires not only extensive field research, but also an understanding of the mechanisms that link fauna and their effects on nutrient cycling. Biological and ecological modeling studies are a powerful tool for understanding those mechanisms and can be used to explicitly determine the impacts of both the benthic community and the individual organisms within it. Important community aspects include 1) organism arrangement and distribution, 2) organism behavior and community succession, and 3) benthic community diversity. Understanding the impacts of these factors is a crucial link in understanding the system-scale effects of water pollution, eutrophication, and global change.