Rice plants are known to be silicon (Si) accumulators, hence farmers often use specific commercial chemical fertilizers to meet the nutrient needs of plants. Farmers commonly use fertilizers that are expensive and produce immediate effects, yet they contaminate the soil, water, and air. We should reduce the use of chemical fertilizers by combining a part of them with alternative organic and biological sources of Si, such as rice husk and Bacillus mucilaginosus (Si-solubilizing bacteria). Furthermore, it rationalizes chemical fertilizer consumption, reduces environmental pollution, and improves nutrient use efficiency to achieve rationalization of consumption with economic benefits in spending and rationalization of consumption of chemicals polluting the environment. In two successive growth seasons, 2021 and 2022, a field experiment was conducted to determine the effects of chemical, organic, and biological silicon fertilization in physiological studies of Egyptian Japonica green super rice. A randomized complete block design was used, with four replications, and the following treatments were used: T1, recommended dose of silica gel (SG; chemical Si); T2, recommended dose of rice husk (RH; organic Si); T3, recommended dose of Si-solubilizing bacteria (SSB; Bacillus mucilaginosus; biological Si); T4, ½ SG + ½ RH; T5, ½ SG + ½ SSB; T6, ½ RH + ½ SSB; T7, 1/3 SG + 1/3 RH + 1/3 SSB; T8, zero chemical, organic, and biological Si (control). The results showed that the application of silica gel as a chemical Si fertilizer, rice husk as an organic Si fertilizer, and Bacillus mucilaginosus as a Si-solubilizing bacteria or biological Si fertilizer source resulted in significantly higher yields of grain (10.71 and 10.53) t ha−1 and straw (12.66 and 12.37) t ha−1 in 2021 and 2022, respectively. Following that, silica gel, when combined with Si-solubilizing bacteria, led to increases in grain yield output of 10.32 and 10.39 t ha−1 and straw yield of 12.16 and 12.05 t ha−1 in 2021 and 2022, respectively. In addition, yield attributes, chlorophyll content in leaves, flag leaf area, flag leaf weight, chlorophyll in flag leaf, crop growth rate (CGR), relative growth rate (RGR), net assimilation rate (NAR), and silicon uptake in grain and straw were determined as follows: The application of silica gel as a chemical Si fertilizer, rice husk as an organic Si fertilizer, and Bacillus mucilaginosus as a Si-solubilizing bacteria or biological Si fertilizer source had a substantial impact on all examined characteristics. According to the optimal treatment, one part of the three parts of Si fertilization utilized just chemical Si fertilizer and the other two parts organic and biological Si. So we can minimize chemical fertilizer use and reduce soil pollution. The findings of this study will be valuable for future research, such as the usage of alternative organic and biological sources of Si in rice.