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.

Short-range communication happens through the 433 MHz Radio Transceiver. 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 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.