The article describes a highly trustable environmental monitoring system employing a small scalable swarm of small-sized marine vessels equipped with compact sensors and intended for the monitoring of water resources and infrastructures. The technological foundation of the process which guarantees that any third party can not alter the samples taken by the robot swarm is based on the Robonomics platform. This platform provides encrypted decentralized technologies based on distributed ledger tools, and market mechanisms for organizing the work of heterogeneous multi-vendor cyber-physical systems when automated economical transactions are needed. A small swarm of robots follows the autonomous ship, which is in charge of maintaining the secure transactions. The swarm implements a version of Reynolds’ Boids model based on the Belief Space Planning approach. The main contributions of our work consist of: (1) the deployment of a secure sample certification and logging platform based on the blockchain with a small-sized swarm of autonomous vessels performing maneuvers to measure chemical parameters of water in automatic mode; (2) the coordination of a leader-follower framework for the small platoon of robots by means of a Reynolds’ Boids model based on a Belief Space Planning approach. In addition, the article describes the process of measuring the chemical parameters of water by using sensors located on the vessels. Both technology testing on experimental vessel and environmental measurements are detailed. The results have been obtained through real world experiments of an autonomous vessel, which was integrated as the “leader” into a mixed reality simulation of a swarm of simulated smaller vessels.The design of the experimental vessel physically deployed in the Volga river to demonstrate the practical viability of the proposed methods is shortly described.