Industrial systems always prefer to reduce their operational expenses. To support such reductions, they need solutions that are capable of providing stability, fault tolerance, and flexibility. One such solution for industrial systems is cyber physical system (CPS) integration with the Internet of Things (IoT) utilizing cloud computing services. These CPSs can be considered as smart industrial systems, with their most prevalent applications in smart transportation, smart grids, smart medical and eHealthcare systems, and many more. These industrial CPSs mostly utilize supervisory control and data acquisition (SCADA) systems to control and monitor their critical infrastructure (CI). For example, WebSCADA is an application used for smart medical technologies, making improved patient monitoring and more timely decisions possible. The focus of the study presented in this paper is to highlight the security challenges that the industrial SCADA systems face in an IoT-cloud environment. Classical SCADA systems are already lacking in proper security measures; however, with the integration of complex new architectures for the future Internet based on the concepts of IoT, cloud computing, mobile wireless sensor networks, and so on, there are large issues at stakes in the security and deployment of these classical systems. Therefore, the integration of these future Internet concepts needs more research effort. This paper, along with highlighting the security challenges of these CI’s, also provides the existing best practices and recommendations for improving and maintaining security. Finally, this paper briefly describes future research directions to secure these critical CPSs and help the research community in identifying the research gaps in this regard.