Wild pigs are an invasive species that significantly impact local ecosystems, agriculture, and public health. One public health concern is fecal contamination of water, as wild pigs can carry pathogenic enteric bacteria. Efforts in the USA to control wild pigs have been hindered by their high fecundity, leading to quick reestablishment in previously inhabited areas and introduction into new landscapes. Therefore, to detect both wild pig presence and absence necessitates effective monitoring methods to assess eradication success, potential population reestablishment, and introduction. Environmental DNA (eDNA) in water has been used for assessing wild pig populations, but microbial source tracking (MST) markers present a promising alternative due to their potential for high sensitivity and specificity. Unlike eDNA, MST specifically identifies fecal contamination, making it a reliable indicator of public health risks associated with pigs. This study aimed to compare the sensitivity of eDNA and MST assays for detecting pigs in an estuarine system and evaluate the viability of the MST assay as a detection method. Water samples were collected monthly from the San Juan Bay Estuary (SJBE) from May 2021 to December 2023. DNA was extracted and analyzed for pig mitochondrial DNA (eDNA) and pig-specific Bacteroidales (MST) using qPCR. The assays' effectiveness were assessed by comparing percent detection frequencies (PDF) during high and low pig population periods across three zones in the SJBE. The zone with the highest pig removal (800+) showed meaningful correlations with both assays. While both assays had comparable PDF during periods of high pig populations, eDNA also exhibited high PDF during low population periods, however only MST significantly correlated with pig populations changes. In the other two zones with fewer pigs removed (<200), MST demonstrated higher detection frequencies. These findings demonstrate the complementarity of both assays and support the viability of MST as an alternative to eDNA for detecting pigs in urban estuarine environments.