The demand of wireless sensor networks (WSNs) is on the raise due to its potential applications. The data transmission occurs via a wireless link by the sensor node in network hence these nodes are vulnerable to several outside or inside attacks. A WSN may works in an unfriendly environment therefore it is a fundamental requirement of WSN to secure the sensing data. In this paper, we focus on highlighting the security issues in a multi-layer WSN architecture and provide a secure communication solution (combination of various state- of-art protocols) for it by considering the WSN constraints. We propose a multi-level protocol distribution method to enhance the security of the WSN under consideration via targeting and providing resilience to specific attacks at each level. The simulation and results show that by implementing our proposed method, the overall security of the network has been enhanced.