Flood and drought events cause significant freshwater inflow fluctuations in estuaries, potentially leading to physiological stress and altered abundances of pathogens such as Vibrio vulnificus and Perkinsus marinus in oysters. To assess the effects of freshwater pulses to oyster reefs in subtropical estuaries in Texas, this study accomplished two goals: 1) reconstructed a reef-specific history of freshwater pulses through shell stable isotope analysis, 2) quantified the abundance of V. vulnificus and P. marinus through culture-dependent and culture-independent microbiology analyses. Oysters from a low-relief and high-relief reef experienced similar fluctuations in shell isotopes, indicating similar ranges of past environmental conditions. V. vulnificus and P. marinus were detected throughout the study but the abundance of these microorganisms was not correlated with environmental parameters or one another. Importantly, the P. marinus infection intensity was always lower at the high-relief reef, which suggests that high-relief reefs may experience lower infection frequencies.