In recent years, the Internet of Things (IoT) has experienced considerable developments and has played an important role in various domains such as industry, agriculture, healthcare, transportation, and environment, especially for smart cities. Along with that, wireless sensor networks (WSNs) are considered to be important components of the IoT system (WSN-IoT) to create smart applications and automate processes. As the number of connected IoT devices increases, privacy and security issues become more complicated due to their external working environments and limited resources. Hence, solutions need to be updated to ensure that data and user privacy are protected from threats and attacks. To support the safety and reliability of such systems, in this paper, security issues in the WSN-IoT are addressed and classified as identifying security challenges and requirements for different kinds of attacks in either WSNs or IoT systems. In addition, security solutions corresponding to different types of attacks are provided, analyzed, and evaluated. We provide different comparisons and classifications based on specific goals and applications that hopefully can suggest suitable solutions for specific purposes in practical. We also suggest some research directions to support new security mechanisms.