Microbial communities of Bacteria, Archaea, and Fungi are known to play integral roles in phosphorus (P) biogeochemical cycles. P is a vital ecosystem nutrient due to its utilization in many of the biological molecules and processes necessary for life. P is generally considered a limiting nutrient and a sudden influx or overabundance of it can cause drastic ecosystem effects. Stream systems are particularly sensitive to P inputs, primarily anthropogenic inputs, and suffer sever effects such as eutrophication as a result. The enclosed chapters take an in-depth look at microbial communities from all three taxonomic groups within stream and unique wetland environments representing P gradients or potentially unique P environments. We first characterize and investigate the relationships of microbes existing in the open water column to their local environment as well as environmental P. We then build on this foundation using functional metagenomics to explore microbial P cycle gene relationships to each other and then directly to environmental P. Throughout this process, we utilize frontier technologies, methods, and statistics to help elucidate these complex relationships. We further introduce new methods and analyses such as the System Relation Overview of Gene Grouping (SROGG) and compare and contrast some existing methods for investigation like computational functional predictions and functional microarray analyses. Compiled, these studies offer a clearer picture of the quasi-mechanics of environmental microbial P cycling. They also highlight the magnitude of gap that exists relating to this type of study and offers a doorway along with tools for further research into the field.