Current networking architectures and communication protocols used for Wireless Sensor Networks (WSNs) have been designed to be energy efficient, low latency, and long network lifetime. One major issue that must be addressed is the security in data communication. Due to the limited capabilities of low cost and small sized sensor nodes, designing security-based networking architectures and communication protocols present a difficult challenge. Commonly used encryption schemes are computation intensive and require large memory. Therefore, achieving security for WSNs needs unique approaches. In this dissertation research, a heterogeneous wireless sensor network (HWSN) is considered, where, while most nodes called low-end nodes are resource limited a few nodes called high-end nodes can have more energy and stronger processing and communication capability and longer communication that can be used to relax the resource bottleneck. A joint design approach that takes advantage of the benefits of a HWSN is proposed. The joint design approach begins first with the design a security oriented reconfigurable hierarchical networking architecture. In this architecture, the HWSN is divided by the high-end nodes into regions, the low-end nodes in each region are divided by clusters, and high-end nodes and cluster heads form a routing/relay backbone. The security oriented architecture is then coupled with the design of a resource efficient secure communication system that uses both public and symmetric key cryptography for data encryption and decryption. The proposed secure communication system requires only a small number of encryption keys to achieve secure communication. The proposed system is evaluated by storage, time complexity, energy consumption, and security requirements based on commercial hardware. The evaluation and simulation results show that the joint design of robust networking architecture and a secure communication scheme is very successful. Robust networking architecture can be formed and reconfigured in a time and energy efficient manner. Data communication/relay is time and energy efficient. The secure communication scheme uses a small storage of keys and it satisfies the security requirements of data confidentiality, freshness, integrity, and authentication. The proposed system is benchmarked with an existing networking architecture and security scheme proposed for HWSNs. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]