The newly constructed Bois d’Arc Lake Reservoir in Fannin County, Texas, USA, inevitably flooded a large ground surface area (67.34 km2) when the reservoir began impounding water in April 2021. Inside this (now) flooded area, land-based archaeological data recovery investigations discovered and documented several archaeological sites, now registered in the state of Texas; though, only two neighboring sites, namely, 41FN178 and 41FN244, are examined here. The first phase of archaeological testing at these sites included shovel testing, test unit excavations, and geoarchaeological trenching that yielded archaeological artifacts suggesting that Middle Caddo Indian peoples (AD 1200–1400) might have occupied this landscape. As the sites were recognized before the reservoir’s impoundment phase, this merited a non-invasive, non-destructive, high-resolution near-surface geophysical study to map strategic areas within sites 41FN178 and 41FN244 that might yield potential shallow targets of archaeological context. The adopted geophysical survey comprised 3D direct current electrical resistivity imaging (ERI) and land horizontal magnetic gradiometry (HMG), each mapping a total surface area of 2133 and 15,640 m2, respectively. The combination of 3D ERI and land HMG surveys was instrumental in rapidly mapping the horizontal and vertical extent of shallowly buried anomalies within a large area prior to the completion of the dam and the beginning of water impoundment. Based on the geophysical insights, the outline of several Caddo houses with functional internal and external features (e.g., burnt cooking surfaces, storage pits, refuse pits, fired soil, ditches, a dump site, and a compound fence) are thought to exist within the uppermost 2 m of the Quaternary stratigraphy at both sites. At site 41FN244, 3D ERI found numerous resistive anomalies surrounding a conductive anomaly, collectively interpreted as a group of post-holes surrounding the remains of a Caddo house’s inner clay floor. It also found a cluster of several resistive anomalies interpreted as midden or middens. The HMG survey carried across areas from which archaeological test units also yielded positive findings, at sites 41FN178 and 41FN244, identified numerous scattered monopolar and dipolar anomalies interpreted as post-molds of Caddo houses, compound enclosures or fences, and adjacent middens. Archaeological excavations guided by the geophysical results yielded significant cultural material and post-mold features at site 244, which validate the geophysical interpretation in a preliminary context. Additionally, several dispersed magnetic anomalies are thought to be shallowly buried hearths, burn cooking surfaces, storage pits, and ditches. The mapped magnetic anomalies agree with the location and distribution of previously found archaeological artifacts and the extent of resistive and conductive resistivity anomalies. Follow-up archaeological excavations of these geophysical anomalies have preliminarily confirmed interpretations.