We investigated the relationship between the geothermal activity and fracture networks that control storage and fluid pathways of geothermal systems in the northern part of the Malawi Rifted Zone (MRZ). It is suggested that low to medium temperature geothermal systems in the MRZ are mainly non-magmatic and structurally controlled. However, structural controls and favorable settings of geothermal activity are poorly understood in this region. We used an approach of remote sensing and aeromagnetic data analysis to 1) identify and characterize fracture networks to better understand the structural controls of geothermal activity in the northern part of the rift, 2) quantify and identify permeable areas using topological analysis of fracture intensity and connectivity frequency proxies, 3) understand the role that inherited structures play in the geothermal systems of the northern part of the rift, and 4) build preliminary geothermal conceptual models of selected geothermal systems. Our findings show that fracture networks in the Karonga and Nkhata regions comprise a varying degree of complexity along strike. This structural complexity occurs mainly in favorable structural settings such as 1) two fault segments coalescing to form hard and soft-linked relays, 2) two different oriented fracture segments intersecting each other, and 3) on the tips of major normal faults. The hot springs are located where one or more of these favorable settings occur. The remote sensing analysis shows that Quaternary normal faults are the primary controlling structures of thermal waters at shallow depths in the Karonga (NW-SE to N-S strike) and Nkhata (N-S strike) regions. The aeromagnetic data revealed that permeable NW-striking foliation planes of the Precambrian Mugesse Shear Zone and WNW to ENE-striking foliation planes of the Mwembeshi Shear Zone are important structural controls of geothermal fluids at greater depths in the Karonga and Nkhata region, respectively. The Mwankeja-Mwesia and Chiweta geothermal systems in the Karonga region show favorable structural settings for geothermal fluids related to NNW and NW-striking normal faults segments that coalesce to form hard and soft-linked relay ramps and NW, and NNE -striking faults intersecting each other and NW-striking foliation planes. The Mtondolo geothermal area in the Nkhata region shows that the intersection of N-striking normal faults and ENE-striking foliation planes is the favorable structural setting that controls the emergence of hot springs through the surface. We conclude that high fracture intensity and connectivity are related to the location of the hot springs at the surface and can be used to determine permeable zones and hidden geothermal fluids together with other methodologies. The aeromagnetic data analysis suggested that buried faults and inherited structures (e.g., foliation planes) are controlling the geothermal fluids at depth. Additionally, our aeromagnetic analysis of magnetic basement depth estimation suggests that some of the geothermal reservoirs in the northern part of the MRZ could have an estimated depth of ~ 500 to 1000 m.b.g.l. Finally, the low-cost methodology applied in this study can reduce the risk of drilling non-productive wells in the early exploration stages and become an exploration strategy for similar geothermal systems in countries of the Western Branch of the East African Rift System.