Global Navigation Satellite Systems (GNSS) is the technology of choice for outdoor positioning purposes but has many limitations when used in safety-critical applications such Intelligent Transportation Systems (ITS) and Unmanned Autonomous Systems (UAS). Namely, its performance clearly degrades in harsh propagation conditions and is not reliable due to possible attacks or interference. Moreover, GNSS signals may not be available in the so-called GNSS-denied environments, such as deep urban canyons or indoors, and standard GNSS architectures do not provide the precision needed in ITS. Among the different alternatives, cellular signals (LTE/5G) may provide coverage in constrained urban environments and Ultra-Wideband (UWB) ranging is a promising solution to achieve high positioning accuracy. The key points impacting any time-of-arrival (TOA)-based navigation system are (i) the transmitters’ geometry, (ii) a perfectly known transmitters’ position, and (iii) the environment. In this contribution, we analyze the performance loss of alternative TOA-based navigation systems in real-life applications where we may have both transmitters’ position mismatch, harsh propagation environments, and GNSS-denied conditions. In addition, we propose new robust filtering methods able to cope with both effects up to a certain extent. Illustrative results in realistic scenarios are provided to support the discussion and show the performance improvement brought by the new methodologies with respect to the state-of-the-art.