© 2019 by the authors. Licensee MDPI, Basel, Switzerland. The proliferation of inter-connected devices in critical industries, such as healthcare and power grid, is changing the perception of what constitutes critical infrastructure. The rising interconnectedness of new critical industries is driven by the growing demand for seamless access to information as the world becomes more mobile and connected and as the Internet of Things (IoT) grows. Critical industries are essential to the foundation of today’s society, and interruption of service in any of these sectors can reverberate through other sectors and even around the globe. In today’s hyper-connected world, the critical infrastructure is more vulnerable than ever to cyber threats, whether state sponsored, criminal groups or individuals. As the number of interconnected devices increases, the number of potential access points for hackers to disrupt critical infrastructure grows. This new attack surface emerges from fundamental changes in the critical infrastructure of organizations technology systems. This paper aims to improve understanding the challenges to secure future digital infrastructure while it is still evolving. After introducing the infrastructure generating big data, the functionality-based fog architecture is defined. In addition, a comprehensive review of security requirements in fog-enabled IoT systems is presented. Then, an in-depth analysis of the fog computing security challenges and big data privacy and trust concerns in relation to fog-enabled IoT are given. We also discuss blockchain as a key enabler to address many security related issues in IoT and consider closely the complementary interrelationships between blockchain and fog computing. In this context, this work formalizes the task of securing big data and its scope, provides a taxonomy to categories threats to fog-based IoT systems, presents a comprehensive comparison of state-of-the-art contributions in the field according to their security service and recommends promising research directions for future investigations.