Are watershed processes controlling the yield, transport, and transformation of carbon, nitrogen, and phosphorus scientifically understood and amenable to man's control in an ecological management framework. For many large estuarine ecosystems such as the Hudson, Chesapeake Bay, and Pamlico Sound, the major contribution of nutrients is from numerous sources within the terrestrial portion of the estuarine watershed. The watershed's topography, geology and hydrology along with land use greatly influences the nutrients yield, transport and transformation. The yield and flux rates can often vary by two orders of magnitude among sub basins within a watershed. The large variability observed in nitrification rates, denitrification rates, carbon yield, etc. suggest possible mechanics for management if one can determine controlling factors and if man can target practices based on optimal use of natural processes to manage nutrients on watershed bases. Presented in the paper are some suggested concepts and insights which could possibly enhance the selection and evaluation of best management practices, forestry practices, urbanization practices, etc., leading to total watershed nutrient management.