Renewable and sustainable energy sources can play an important role in meeting the world’s energy needs and also in addressing environmental challenges such as global warming and climate change. Geothermal well-doublet systems can produce both electrical and thermal energy through extracting heat from hot-water aquifers. In this paper, we examine some potential challenges associated with the operation of well-doublet systems, including heat conductivity, chemical, and mechanical issues. In these systems, geomechanics issues such as thermal short-circuiting and induced seismicity arise from temperature and pressure change impacts on the stress state in stiff rocks and fluid flow in fractured rock masses. Coupled chemical processes also can cause fluid channeling or formation and tubular goods plugging (scaling) with precipitates. Mechanical and chemical disequilibrium conditions lead to increased production uncertainties; hence risk, and therefore coupled geo-risk assessments and optimization analyses are needed for comparative commercialization evaluations among different sites. The challenges related to heat transfer processes are also examined. These studies can help better understand the issues that may arise during the operation of geothermal well-doublet systems and improve their effectiveness, subsequently reducing associated costs and risks.