Wireless sensor networks (WSNs) have demonstrated research and developmental interests in numerous fields, like communication, agriculture, industry, smart health, monitoring, and surveillance. In the area of agriculture production, IoT-based WSN has been used to observe the yields condition and automate agriculture precision using various sensors. These sensors are deployed in the agricultural environment to improve production yields through intelligent farming decisions and obtain information regarding crops, plants, temperature measurement, humidity, and irrigation systems. However, sensors have limited resources concerning processing, energy, transmitting, and memory capabilities that can negatively impact agriculture production. Besides efficiency, the protection and security of these IoT-based agricultural sensors are also important from malicious adversaries. In this article, we proposed an IoT-based WSN framework as an application to smart agriculture comprising different design levels. Firstly, agricultural sensors capture relevant data and determine a set of cluster heads based on multi-criteria decision function. Additionally, the strength of the signals on the transmission links is measured while using signal to noise ratio (SNR) to achieve consistent and efficient data transmissions. Secondly, security is provided for data transmission from agricultural sensors towards base stations (BS) while using the recurrence of the linear congruential generator. The simulated results proved that the proposed framework significantly enhanced the communication performance as an average of 13.5% in the network throughput, 38.5% in the packets drop ratio, 13.5% in the network latency, 16% in the energy consumption, and 26% in the routing overheads for smart agriculture, as compared to other solutions.