Changes in freshwater inputs due to water diversions and increased urbanization may alter the function and properties of estuarine ecosystems in South Texas. Freshwater and nitrogen inputs from the Mission and Aransas rivers to the federally designated Mission-Aransas National Estuarine Research Reserve (Mission-Aransas NERR) have received considerable attention in the past few years. However, freshwater inputs from two rivers (the San Antonio and Guadalupe rivers) that combine and drain into a neighboring bay (San Antonio Bay) may also provide a substantial nitrogen source to Aransas Bay, which is within the boundaries of the Mission-Aransas NERR. In order to study the influence of the San Antonio and Guadalupe rivers, an oyster species, Crassostrea virginica, was chosen to provide time-integrated information about freshwater contribution as a nitrogen source within the bays. Chapter One addresses variations in isotope values ([delta]¹⁵N and [delta]¹³C) in oyster adductor muscle tissue from 2009-2011 along a sampling transect from the head of San Antonio Bay through Aransas Bay. Stable carbon isotope values increased linearly from approximately -25 % to -17 %, while stable nitrogen isotope values decreased from approximately +16 % to +10 % along this transect. The patterns in stable carbon and nitrogen isotope values are consistent with substantial mixing of river-supplied water and nitrogen from San Antonio Bay into Aransas Bay. Variations in nitrogen isotopic signature between periods of sustained drought and flood conditions were relatively small, suggesting that riverine nitrogen contributions were similar regardless of the amount of freshwater inflow observed during the time frame of this study. Chapter Two addresses the isotopic equilibration time for adult oyster adductor muscle tissue using a year-long transplant experiment (November 2010-November 2011). Full representation of ambient water isotopic composition in oyster adductor muscle tissues was determined to occur roughly a year after transplant. Oyster adductor muscle could therefore be useful for long-term monitoring of nitrogen contribution from freshwater sources, and would be valuable to include in concert with water sampling and analysis of other tissues that have shorter integration rates for a comprehensive view of an estuarine system. / text