The Internet of Things (IoT) era is evolving into sensor initiated, actuation-driven, and machine intelligence-based decision making platform for smart cities. A smart city system aims at a seamless and secure interconnection of sensors, actuators, and data processing resources to ensure digital, efficient, and reliable services. In this article, we present a brief planar overview of a smart city system architecture by introducing the application, sensing, communication, data, and security/privacy planes. Tailoring existing communication protocols and infrastructures to bridge massively deployed sensors and data processing/storage resources introduces unique communication challenges for smart cities. Furthermore, co-existence, integration, and control of dedicated and non-dedicated sensors is a grand challenge while IoT sensors continuously push sensory data through the communication medium towards data processing and analysis planes. While pervasiveness and ubiquity of smart city services are ensured by the interaction of communication and sensing technologies, their robustness and resilience call for customized security and privacy solutions. With these in mind, we focus on sensing/actuation, communication, and security planes of a smart city system and present a comprehensive survey of the challenges and state-of-the-art solutions in each plane. Furthermore, we provide insights for open issues and opportunities in these planes.