Currently, agriculture based on agronomic greenhouses is replacing traditional agriculture. This technique reduces dependence on rain on crops. It also generates a controlled internal environment making optimal use of land and water resources. However, this environment needs more care and attention compared to traditional agriculture. To overcome this limitation, various radio frequency (RF)-based technologies can be used. Nevertheless, studies show that the use of communications in RF bands degrades crops' growth and quality. Therefore, an efficient solution is to use the visible light spectrum for communication, the main technology of which is called visible light communication (VLC). Despite numerous studies for the application of VLC in indoor environments, specific VLC systems for agronomic greenhouse environments or their channel models are not yet investigated in depth. To collaborate on state of art on this topic, we present in this paper a novel channel model that incorporates specific factors that affect the quality of VLC systems in agronomic greenhouse environments. Factors such as the random position and orientation of the transmitters and external environmental agents such as atmospheric and different noise types are considered. These components are integrated into an analytical framework by developing the mathematical model of the VLC channel. Furthermore, the analytical expressions of the received power, the signal-to-noise-ratio (SNR), and the bit error rate (BER) are obtained. A VLC system applied to an agronomic greenhouse scenario is developed through computer simulations to validate the mathematical analysis. The results show that illuminance is adequate for the efficient operation of the greenhouse. Besides, the influence of atmospheric factors and noises on the magnitude and temporal dispersion of the channel impulse response is verified. Finally, the results show the system's performance in terms of SNR and BER, observing their differences compared to a traditional indoor VLC system.