I'm not getting the USB transfer rates I expected

A few factors can contribute to lower than advertised USB (or Thunderbolt™) performance from connected devices. Affected devices can include portable SSDs, USB flash drives, or SSDs being used in external enclosures or on an external adapter. Below are solutions to several of these factors, which can be easily addressed by an end user for an immediate performance boost to the attached hardware. 

Multiple standards may be featured on a system or motherboard. For best performance, refer to your system or motherboard documentation to identify and connect your storage device to the port with the highest speed standard available to you. If an older standard is used, maximum performance will be limited to what that standard can support. The table below summarizes USB standards for storage devices and theoretical maximum speeds of connected devices.

Note: These transfer protocols have electrical overhead and while theoretically will equal listed speeds above, due to overhead these speeds will never be reached.

As seen above, older USB standards will limit SSD performance. Besides the ports, an enclosure or other adapter can bottleneck this transfer rate. Verify the specifications of your enclosure and cables to ensure they comply with a standard operating at your desired speed.

Multiple USB devices connected through the same controller will see their speed split between them when they are under load simultaneously. Ports related in this way may not be obvious at a glance, but will typically be adjacent to one another on a system or motherboard. Devices run through a USB hub and into a single USB port on a system will be affected similarly.
Ports can also split power across multiple devices on the same controller. While this won't directly affect speed, when multiple devices begin reducing power necessary for others to function abnormal performance of the devices can be seen, such as devices ceasing to function or "disappearing" from the operating system (OS) and other applications. 

Modern OSes support the USB 3 standard by default, but legacy OSes including Windows 7 and earlier will require USB 3 drivers to be downloaded and installed to allow connected devices to work properly. If not done automatically by an OS update process, go to your system or motherboard manufacturer's website, then find and install the driver for your USB controller to allow full compatibility with USB 3 devices.
While not necessary, using these manufacturer drivers may enhance performance of USB devices even in operating systems with native support for USB 3. You may find that the default OS drivers for USB 3 perform more slowly than ones supplied by your hardware manufacturer.