There are several communication links between the USV and the remote operator station. Between level 1 and the remote operator station, there are two communication links: An Iridium system and a short-range radio system. The Iridium system is intended as a fallback solution in case of failure of the level 2 system. Iridium is the only satellite communication system provider with global coverage and is known for high-reliability. The selected Iridium transceiver is for short burst data (SBD) and will allow for reporting of parameters such as the state of the onboard systems and the USVs position, but also the ability for the remote operator to send simple commands to the onboard system. The short range radio system will be used for manual control of the USV during launch and retrieval.

Direct communication for telemetry happens through the OWL radios. The operator is able to send commands encoded in NMEA format. The messages the Operator can send to Level 1 respect this format:
;#; RCC01 , RUD , THR , Kp , Ki , PWR_SETT , FALLB_MODE , MANUAL_CTRL ;#; Where:
- RCC01 is the msg ID;
- RUD is the rudder angle [-450,450];
- THR is the thruster intensity [-100,100];
- Kp and Ki set the gains for the Level 1 Fallback Autopilot;
- PWR_SETT are the power settings: 6-bits string where 1 disables and 0 enables;
- FALLB_MODE selects the fallback mode: 0 for rudder 0, 1 for circle, 2 for autopilot;
- MANUAL_CTRL is a boolean: 1 for taking control (manual), 0 for giving control (autopilot).

The Owl VHF is a small, yet high performance radio transceiver packed with features. It's very flexible internal architecture allows a wide variety of modulation types and encoding. Rather than the typical SDR approach where samples are processed by an external device, the Owl does all its processing internally. A large command set regarding modulation, encoding and user protocol is configured through a serial port.
;#; ;#;

The communication happens through Neptus interface. A Java-based plugin provides the Operator with a real-time monitoring of the AutoNaut status and all the Level 1 subsystem.

Through the visual interface in Neptus the Operator is able to enable/disable sensors and subsystems. Each choice is then encoded in a NMEA message and sent through 433 MHz Radio. The Operator is also able to monitor the reception and application of the sent instructions through the ack message sent back by Level 1.

Satellite communication between Level 1 and the Operator is a fallback channel. It is meant to be triggered in specific emergency occasions in which urgent and essential messages need to be communicated to the Operator, i.e. the failure of a sensor or subsystem. Also, the AutoNaut may sail in areas where any 4G coverage is available. If this is the case, the Operator can benefit from satellite communication for sending instructions and plans to the AutoNaut. Satellite communication happens through Iridium, described in the Level 1 Sensors section.
The communication interface to the device consists of serial communication at RS-232 voltage levels. The baud rate is configurable. The device uses 8 data bits and 1 stop bit. In addition to the serial interface, the device has a ring alert signal wire, a network availability signal line and a sleep mode line. Only the sleep mode line will be used in the system.
When the Campbell Scientific C6 computer sends a message to the RockBlock device, the message is loaded into the so-called mobile originated message buffer in the device. A message transfer session between the RockBlock and the gateway SBD subsystem is then initiated. The RockBlock will notify the CR6 on the success of the message. If the RockBlock receives a message, it will be stored in the mobile terminated buffer in the device and can be transferred to the CR6 via the serial interface. The communication between the Iridium unit in the rock block and the CR6 level 1 computer follows an Iridium proprietary protocol that is described in a document called ISU AT Command Reference. A total of 180 commands are described, in which roughly 50 are supported by the Iridium 9602 transceiver. Out of those commands, 20 concern the handling of short burst data service. After assessing the different functions and possibilities, the following instructions were selected for implementation:

- SBDI (Short Burst Data Initiate);
- SBDRT (Short Burst Data Read Text);
- SBDRB (Short Burst Data Read Binary);
- SBDS (Status);
- SBDTC (Transfer MO to MT);
- SBDWB (Write binary);
- SBDWT (Write text).

The RockBLOCK device is IP68 rated and hosts an Iridium 9602 unit, an antenna and a voltage regulator. The 9602 unit is interfaced with RS-232 using AT commands. Depending on the conditions, the unit can send or receive a message approximately every 40 seconds. The cost is 0.1 to 0.05 GBP per 50-byte message, depending on the bundle that is bought. In addition, there is a 10 GBP line rental per month. The system has a limited bandwidth and is therefore only suitable for simple control monitoring or tracking applications. The maximum package sizes are 340 bytes for sending and 270 bytes for receiving. Although the latency is typically a few seconds, it may be as much as a minute or more.