The Rio Sonoyta, despite grazing across the watershed, agriculture, groundwater pumping, and the incredible dry nature of the region, still has perennial flow in stretches west of the town of Sonoyta. These areas supports the native Quitobaquito Pupfish (Cyprinodon macularius eremus) and the Rio Sonoyta Mud Turtle (Kinosternon sonoriense longifemorale).
Much of the bottomland, especially in the middle stretches of the watershed, has been cleared for agriculture. Grazing can be severe in some parts of the watershed, made worse by the extreme dryness of the region. The river channel cuts south a little west of Sonoyta abutting the Pinacate lava fields.
Mesquite bosques with huge trees existed along the Rio Sonoyta and were said to have been an amazing sight into the 1900's, before they were cleared.