The primary goal is to understand potential contaminant stress on ecosystems in both natural (reference systems) and stressed environments (e.g. anthropogenically compromised). Parts of this research program are focused on the further development & application of novel environmental tools for assessing contaminants in terrestrial and aquatic ecosystems within the Great Lakes basin, and in other parts of Canada and the world. In many cases, the activity of microorganisms will directly impact the chemical conditions in both surface and subsurface water column and sediment environments controlling the fate of nutrients and contaminants alike. Questions arise such as what are the baselines or reference systems that can be used. What indices can be used to study the long-term and short-term controls on the mobility, cycling, and bioavailability of toxic metals and organic contaminants? In many cases the balance of chemical oxidizing and reducing components in water will control the development of chemical and nutrient gradients observed in either natural and/orapplied systems (e.g. constructed wetlands or bioreactors). In these cases, biogeochemical systems will determine the direction and onset of specific metabolic pathways as defined by their favorable thermodynamic outcome, an issue for most bioremediators (i.e. microorganisms). Also, the degree of chemical alteration (toxicity or degradation products) can be directly linked to the proportion of their biological activity. Over the course of this century, it will be important to identify cost effective/low maintenance solutions for treating contaminants and nutrient flux in Canada’s watersheds.