Space navigation, whether for near-Earth satellites or deep space probes orbiting in remote regions of the solar system, rests on precise time and frequency measurements. However, deep space navigation, which cannot rely on the extensive and powerful infrastructure offered by GNSS constellations and the associated ground systems, faces bigger challenges. Measurements are obtained by exchanging radio signals between ground antennas and distant spacecraft, providing in most cases line-of-sight information. The observable quantities used for orbit determination in the solar system can be seen as measurements of angles, distances and velocities, but ultimately all these geometric quantities reduce to precise time and frequency measurements, requiring very stable clocks. State of the art microwave systems are able to deliver accuracies at a level of few cm for range and 10-6 m/s (at 1000 s integration times) for range rate, for a spacecraft located nearly everywhere in the solar system. Angular measurements, based on a VLBI technique called DOR (delta-differential one-way ranging), often attain accuracies at the level of 1 nrad (corresponding to 150 m in the direction orthogonal to the line of sight at 1 AU). Especially if augmented with dedicated instrumentation, microwave tracking systems used for space navigation are also powerful tools for planetary science, in particular for geodesy and geophysics. Most of our knowledge of planetary interiors comes from gravity measurements, enabled radio links with excellent frequency stability. Precise knowledge of solar system dynamics and tests of gravity laws also rely on the same observable quantities. This talk will review the state of the art microwave technologies employed in deep space navigation, planetary geodesy and fundamental physics and offer a perspective view on new methods, including the use of atomic clocks in deep space and largely autonomous navigation infrastructure at Mars and the Moon.