The present study evaluated the application of Ground Penetrating Radar and Electromagnetic Induction geophysical tools combined with sedimentology for the description of the subsurface of sites destined for the installation of ponds for an extensive freshwater fish farming system. Two areas with similar topographic characteristics (flat land near bodies of water) were investigated in the Amazon region of northern Brazil: Area 1—the future site of an aquaculture research center, and Area 2—an established fish farming operation. These tools performed well in the evaluation of the suitability of the terrain for the installation of aquaculture ponds. The application of these tools can, thus, be recommended for aquaculture projects, given that it provides advanced knowledge on the characteristics of the local soils, which is extremely important to guarantee the sustainability of any aquaculture operation. These data can help minimize the environmental impacts of the process, while maximizing the economic returns to the installation of an aquaculture operation.