Pensacola Dam, operated by the Grand River Dam Authority (GRDA), is a multiple-arch buttress dam constructed in 1940. The dam has little or no existing geophysical reports on the integrity of the dam foundation rock and even less knowledge at depth. Visual inspection indicated evidence of seepage at some arches of the dam. As a pilot study, we conducted a suite of geophysical surveys inside two arches (Arch-16 and Arch-17) and a part of the downstream berm to characterize the dam foundation rock, delineate seepage zones, and identify the most appropriate geophysical methods for temporal monitoring of the dam’s conditions. The geophysical methods included electrical resistivity tomography (ERT), self-potential (SP), multichannel analysis of surface waves (MASW), compressional (P)-wave refraction, and shear (S)-wave reflection. Water samples were collected for geochemical analysis to investigate the source of the seepage flow inside Arch-16. The geophysical results characterized the dam foundation rock into an unsaturated limestone and chert overlying a water-saturated limestone and chert. The ERT profiles indicated that groundwater is rising inside the arches and significantly dropping under the downstream berm, which can be due to the uplift pressure beneath the dam base. Zones of high seepage potential were detected near the buttress walls of the two surveyed arches, which may be related to previous blasting, excavation of the dam foundation, concrete placement, or improper grouting. The geochemical analysis of water samples taken from the artesian wells inside Arch-16 and the Grand Lake revealed different chemical compositions, suggesting that the source of water could be a mixture of groundwater and lake water or lake water interacting with rock and reaching the surface through fractures; however, more sampling and further analysis are required to ascertain the source of the seeps. This study showed that the ERT, SP, and S-wave reflection methods have effectively characterized the dam foundation rock and seepage zones beneath the arches. The study provided a better understanding of the conditions of the dam foundation rock, evaluated the utilized geophysical methods, and determined the optimum geophysical methods that can be used for the characterization and monitoring of the subsurface conditions along the entire length of the dam. In this study, we have demonstrated that the integration of effective geophysical surveys and geochemical analysis yielded optimum results in solving a complex dam safety problem. This strategy promotes the best practice for dam safety investigation.