Cyber-attacks long have been a topic reserved for sci-fi movies and books. With the advance of internet and the globalisation of technology supply chains, as well as the growing political and economic pressure around the world, cyber warfare has become the new weapon of choice for covert state operations, but also rogue organizations. In the last 2 decades multiple major industries have suffered some kind of outage – power generation, manufacturing, oil & gas, transport, and others. A typical industrial system is designed for a life span of more than 20 years, making future issues hard to protect against at the planning phase. No widespread efforts exist to identify such threats, to detect attacks and counteract them. This thesis proposes a practical approach for lower level protection of control systems based on linear watermarking as a transparent process to provide detection for any malicious activity that might significantly impact the operations of the plant.