The monitoring of agricultural areas is one of the most important topics for remote sensing data analysis, especially to assist food security in the future. To improve the quality and quantify uncertainties, it is of high relevance to understand the spectral reflectivity regarding the structural and spectral properties of the canopy. The importance of understanding the influence of plant and canopy structure is well established, but, due to the difficulty of acquiring reflectance data from numerous differently structured canopies, there is still a need to study the structural and spectral dependencies affecting top-of-canopy reflectance and reflectance anisotropy. This paper presents a detailed study dealing with two fundamental issues: (1) the influence of plant and canopy architecture changes due to crop phenology on nadir acquired cereal top-of-canopy reflectance, and (2) the anisotropic reflectance of cereal top-of-canopy reflectance and its inter-annual variations as affected by varying contents of biochemical constituents and changes on canopy structure across green phenological stages between tillering and inflorescence emergence. All of the investigations are based on HySimCaR, a computer-based approach using 3D canopy models and Monte Carlo ray tracing (drat). The achieved results show that the canopy architecture significantly influences top-of-canopy reflectance and the bidirectional reflectance function (BRDF) in the VNIR (visible and near infrared), and SWIR (shortwave infrared) wavelength ranges. In summary, it can be said that the larger the fraction of the radiation reflected by the plants, the stronger is the influence of the canopy structure on the reflectance signal. A significant finding for the anisotropic reflectance is that the relative row orientation of the cereal canopies is mapped in the 3D-shape of the BRDF. Summarised, this study provides fundamental knowledge for improving the retrieval of biophysical vegetation parameters of agricultural areas for current and upcoming sensors with large FOV (field of view) with respect to the quantification of uncertainties.