NavList:

Pitot-like speedlogs eventually replaced the brass mechanical "patent" logs towed behind ships that you were asked about earlier.  They were in near-universal usage in WWII. 

Pitot-style tubes were eventually replaced by electromagnetic speedlogs.  As a conductor (such as saltwater) passes through an electromagnetic field a voltage is induced in the water that is proportional to the water velocity.  EM logs are still in use, but have largely been replaced by acoustic systems that measure velocity using the doppler effect.  Acoustic doppler velocity measurement is kind of amazing.  At the high end, a modern Acoustic Doppler Current Profiler (ADCP) can measure three-dimensional currents at a variety of depths up to several hundred meters below the ships.  If in range, ADCPs can also track the seafloor and produce a ground-velocity estimate as well.  State-of-the-art modern underwater drones dead-reckon using seafloor-relative velocities updating at least once per second.  Even with all the inertial and acoustic tracking options available, its amazing how many underwater vehicles still rely on really good dead-reckoning.  Computers, doppler velocity logs, and fiber optic gyrocompasses definitely help.

Naturally, most surface ships use one of several GPS methods to get speed over ground.  We occasionally pick things out of the ocean at work, and have had surprising difficulty explaining the difference between "velocity through water" and "velocity over ground" to some younger licensed mariners.  It seems these days everyone wants to do precision manuvering using a GPS-based dynamic positioning autopilot, which can be very unhelpful when trying to hold position relative to something floating on the surface.  Especially in, say, the gulf stream.