Ionospheric propagation is harmful for the electromagnetic signals broadcast by Global Navigation Satellite System (GNSS) satellites, mainly because of the presence of electron density anomalies. GNSS receivers are indeed of primary importance in scintillation and Total Electron Content (TEC) monitoring, especially at low and high latitudes, where scintillations are more frequent. Professional dual frequency custom hardware Global Positioning System (GPS) receivers have been successfully exploited since years as measurement tools able to provide post-correlation data that are then used for modeling the atmospheric phenomena. Recent trends in scientific GPS receivers implementation consider Software Defined Radio (SDR) as a valuable technology that enables access to intermediate and low level receiver processing stages. With respect to commercial hardware tools, they provide a larger subset of observables related to the signal processing stages, as well as a high grade of flexibility and re-configurability, depending on the user needs. Such features enable the design and test of innovative ionosphere monitoring techniques.