Water retention in earthen fishponds throughout a fish farming cycle is challenging due to climate-induced water loss via evapotranspiration, seepages, and lowering of the groundwater table. These processes depend on the soil hydrostratigraphic condition and constitute a major challenge for fish farmers in the Niger-Delta region of Nigeria, where seasonal variations cause groundwater levels to fluctuate. This study assesses the use of non-invasive geophysical methods, including electrical resistivity and induced polarization, to guide the selection of sites with appropriate hydrostratigraphic conditions for establishing earthen fishponds. We combined measurements of electrical resistivity and chargeability distributions to assess the subsurface of two earthen fishpond sites at Ugono-Abraka and Agbarha-Otor areas in the Niger-Delta region of Nigeria. Electrical soundings were acquired at ten locations, while two-dimensional electrical resistivity and Induced polarization were acquired across five transects using Schlumberger and dipole-dipole electrode configurations. The field data were inverted using IP2win, and Diprowin software. The geophysical models were combined with lithological data from soil cores to characterize the subsurface stratigraphy, while measured clay contents were used to estimate infiltration coefficients relying on established petrophysical relationships. The delineated subsurface properties at Ugono-Abraka and Agbarha-Otor show higher variations than assumed by practitioners. The complementary results of low resistivity (20–140 Ωm) and high chargeability (10–50 msec) revealed areas with clay-rich sediments. Soil samples confirmed higher clay contents of up to 10% at Ugono-Abraka and low values of 2% at Agbarha-Otor. Estimated infiltration coefficients are lower at the Ugono-Abraka site (1.6 m/day) compared to Agbarha-Otor (8.4 m/day). This implies variable water loss in the earthen fishponds; hence, we recommend characterizing these variations using non-invasive geophysical methods before establishing medium to large-scale earthen fishponds in the area.