Loss of seagrass habitat in many parts of the world has been attributed to increases in nutrient loading to nearshore areas. The role of excess epiphyte, macroalgal or phytoplankton growth in shading of seagrass leaves and negatively affecting seagrass health is generally agreed to be a prevalent mechanism in seagrass decline worldwide. In the present study nutrient addition experiments were undertaken at three sites in Western Port, Victoria. Nutrients were added to the water column using the controlled release fertiliser Osmocote™ in late summer 2005. The experiments ran for one month at two of the sites (Blind Bight and Hastings) and at the third site (Crib Point) the experiment ran for three months. Control and nutrient addition plots were monitored for concentrations of inorganic nutrients, number of seagrass leaves, seagrass, epiphyte and loose algal biomass and invertebrate faunal assemblages. Nutrient additions had increased ash free dry weight of seagrass leaves and loose algae at two of the three sites studied. There was also an increase in gammarid amphipod densities at the Crib Point site. We consider that Western Port seagrass habitat is sensitive to increased loads of nutrients within the water column with the Blind Bight region most at risk.