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The utilization of solar energy in thermal energy systems was and always be one of the most effective alternative to conventional energy resources. Energy efficiency is widely used as one of the most important parameters in order to evaluate and compare thermal systems including solar collectors. Nevertheless, the first law of thermodynamics is not solely capable of describing the quantitative and qualitative performance of such systems and thus exergy efficiency is used so as to introduce the systems’ quality. In this work, the performance of a flat plate solar collector using water based nanofluids of different nanoparticle types as a working fluid is analyzed theoretically under the climatic conditions in Greece based on the First and Second Law of Thermodynamics. A mathematical model is built and the model equations are solved iteratively in a MATLAB code. The energy and exergy efficiencies as well as the collector losses coefficient for various parameters such as the inlet temperature, the particles concentration and type are determined. Moreover, a dynamic model is built so as to determine the performance of a flat plate collector working with nanofluids and the useful energy that can be stored in a water tank. The exergy destruction and exergy leakage are determined for a typical day in summer during which high temperatures and solar intensity values are common for the Greek climate.