The Edwards Aquifer serves as a primary source of drinking water to more than 2 million people in south-central Texas. As a karst aquifer, it is vulnerable to human and animal fecal contamination which poses a serious risk to human and environmental health. A one-year study (Jan 2018 – Feb 2019) at 11 sites (6 creeks, 3 ponds, 2 wells) was conducted to determine the primary sources of fecal pollution along the contributing and recharge zones in the Edward Aquifer. Microbial source tracking (MST) assays targeting general (E. coli, Entero1, BacUni), human (HF183, BacHum), and animal (BacCow, BacCan, Chicken-Duck Bac) markers were used. Spatial variations for these fecal markers were analyzed to determine the potential sources of the fecal contaminants. In addition, the impact of precipitation was assessed on the level of these fecal makers to understand the relationship between them. Levels for the three general indicators were highest and exhibited similar trends across the sampling sites, suggesting that the sole use of these markers is not sufficient for specific fecal source identification. Relatively higher levels in human fecal markers were observed at sites having greater human population and septic tank density and may be attributed to leaks or breaks in these infrastructures. Among the animal fecal markers, highest concentrations were observed for pond sites compared to creek and well sites. The samples were divided under "wet" and "dry" weather depending on previous 24 h rainfall. Higher detections were observed in most of the pond and creek sites under "wet" weather, indicating that the non-point sources stormwater runoff contributed fecal contamination to water bodies. The Bacteroidales marker assays, when combined with weather information, can allow for a better understanding of the sources of fecal contamination, which can help devise effective mitigation measures to protect water quality.