The Silway River has historically failed to meet safe fecal coliform levels due to improper waste disposal. The river mouth is located in General Santos City, the tuna capital of the Philippines and a leading producer of hogs, cattle, and poultry. The buildup of contaminants due to direct discharge of waste from chicken farms and existing water quality conditions has led to higher fecal matter in the Silway River. While there were technical reports in the early 2000s about poultry farming, this is the first study where fecal coliform from poultry farming was detected in the Silway River using highly sensitive protocols like qPCR. This study characterized the effect of flow velocity and physicochemical water quality parameters on chicken fecal contamination. Gene markers such as Ckmito and ND5-CD were used to detect and quantify poultry manure contamination through microbial source tracking (MST) and environmental DNA (eDNA) profiling. The results of this study showed the presence of chicken fecal bacteria in all stations along the Silway River. The results revealed that normal levels of water quality parameters such as temperature, pH, and high TSS concentrations create favorable conditions for chicken fecal coliforms to thrive. Multiple regression analysis showed that flow velocity and DO significantly affect chicken fecal contamination. A lower cycle threshold (Ct) value indicated higher concentration of the marker ND5-CD, which means higher fecal contamination. It was found that there was an inverse relationship between the Ct value and both velocity (R2 = 0.55, p = 0.01) and DO (R2 = 0.98, p = 0.2), suggesting that low flow velocity and low DO can lead to higher fecal contamination. Findings of fecal contamination could negatively impact water resources, the health of nearby residents, and surrounding farms and industries, as well as the health and growth of fish.