Ionospheric indices give information about ionospheric perturbations, which may cause absorption, diffraction, refraction, and scattering of radio signals, including those from global navigation satellite systems (GNSS). Therefore, there may be a relationship between index values and GNSS positioning results. A thorough understanding of ionospheric indices and their relationship to positioning results can help monitor and forecast the reliability and accuracy of GNSS positioning and support the precision and safety of life applications. In this study, we present the relationship between three indices: Gradient Ionosphere indeX (GIX), Sudden Ionospheric Disturbance indeX (SIDX), and Rate of Total electron content Index (ROTI) in relation to precise positioning results. We used two approaches: precise point positioning (PPP) and relative positioning for long baselines. We focus on GNSS stations located in Europe for two selected geomagnetic storms: March 17, 2015, and May 22, 2015. Our results show that in the case of PPP, positioning degradation occurred mainly at high latitudes and was mostly caused by rapid small-scale changes in ionospheric electron content represented by SIDX and ROTI. We also showed a significant correlation between cycle slips of GNSS signals and ROTI (0.88). The most significant degradations for relative positioning for low and medium latitudes were associated with large spatial gradients reflected by the GIX.