Phosphorus (P) is a key nutrient required by all living organisms. In freshwater, P can be limiting as it readily adsorbs to particles; however, it is released via desorption in seawater. This makes estuaries—transition zones between land and sea—vulnerable to nutrient-driven eutrophication. However, through mineralization and biological transformations, estuaries can sequester P, rendering a valuable ecosystem service. Yet, processes involved in the retention and cycling of P in estuaries remain poorly understood. In this dissertation, I address critical knowledge gaps by characterizing P forms in sediments and by tracking changes in microbial populations involved in P storage in natural and restored wetland habitats in the Columbia River estuary.