Extreme changes in salinity places severe stress on biotic communities, potentially compromising the development of healthy, sustainable estuarine environments. In southeast Florida, construction of drainage projects for agriculture and urbanization have altered the volume, timing, and distribution of incoming freshwater to the St. Lucie estuary. Past research has suggested that the eastern oyster, Crassostrea virginica, can be effectively used as an indicator for the condition of this ecosystem. Natural pathogens, whose virulence functions in response to several abiotic factors, can also modify an organisms ability to respond appropriately to changes in salinity.A Rapid Change Experiment was conducted to determine responses in C. virginica artificially infected with the protozoan parasite, Perkinsus marinus, following changes in salinity. Responses were measured as changes in condition index and RNA/DNA ratios. Our experiment was designed to test the effects of sequential pulses of low salinity (5 and 2 ppt) on oyster condition. To determine if artificial P. marinus infection in oysters is comparable to infection in natural populations, preliminary work was done using real-time PCR to detect and quantify the amount of P. marinus injected into C. virginica. The method of artificial infection of P. marinus in oysters was significant (p>0.0003) when compared to control oysters, indicating that the method of injection of P. marinus is realistic to environmental infections. Body condition index for non-injected and injected oysters for the Rapid Change Experiment proved to be established more by salinity regimes than P. marinus infection, whereas RNA/DNA ratios appear to be a function of sampling dates and the infection status, due to variability seen in the non-injected control group. The work done here proves useful not only for the St. Lucie estuary but estuaries elsewhere. Stress imposed on an estuary due to salinity pulses can be measured by utilizing the eastern oyster. It is also important to note that P. marinus, also an indicator of estuary stress and proven to be very problematic for C. virginica, can be detected and quantified using recombinant DNA technology.