The paper presents a novel traceability system architecture based on web services, which are used to integrate traceability data captured through Radio Frequency Identification (RFID) systems with environmental data collected with Wireless Sensor Networks (WSN) infrastructure. The solution, suitable to be deployed in Small to Medium Enterprises (SMEs), is provided by integrating information collected along the entire food supply chain, tracking the products from the farm to the consumer. The results of the deployment of the novel system in two pilots in the aquaculture business are also presented, showcasing how business processes in the aquaculture supply chain can be improved by the architecture and flexibility of the new system, since the two companies involved in the project are of very different sizes. Additionally, we present an analysis of the benefits obtained by the introduction of the new system in the companies based on predefined objectives and the evaluation of KPIs. The evaluation of KPIs is presented as the time reduction of activities and can improve the Efficiency of the companies in 89-95%. (C) 2013 Elsevier Ltd. All rights reserved.