All Arduino boards have at least one serial port (also known as a UART or USART): Serial. It communicates on digital pins 0 (RX) and 1 (TX) as well as with the computer via USB. Thus, if you use these functions, you cannot also use pins 0 and 1 for digital input or output.
The Arduino Due has three additional 3.3V TTL serial ports: Serial1 on pins 19 (RX) and 18 (TX); Serial2 on pins 17 (RX) and 16 (TX), Serial3 on pins 15 (RX) and 14 (TX). Pins 0 and 1 are also connected to the corresponding pins of the ATmega16U2 USB-to-TTL Serial chip, which is connected to the USB debug port. Additionally, there is a native USB-serial port on the SAM3X chip, SerialUSB'.
So my question is, if I am not using the USB port for anything aside from uploading my code (ie once the controller is complete and attached to the aquarium) can I use all 4 serial ports for my probes?