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Modern agricultural practices face increasing environmental challenges, most notably the excessive reliance on inorganic chemical fertilizers, which leads to soil fertility degradation and a long-term rise in soil salinity levels. In an attempt to mitigate these effects, farmers often resort to traditional organic fertilizers such as animal manure; however, this alternative is not without negative environmental impacts, particularly the emission of greenhouse gases such as methane and carbon dioxide. In this context, the Sultanate of Oman possesses a rich marine biodiversity that includes various types of marine shells and mollusks, among them the green mussel. These resources are often limited to ornamental and decorative uses, while their underlying biochemical potential and possible applications in sustainable agriculture remain largely overlooked. This study aimed to investigate the effect of using marine shell powder (green mussel shells) as a bio-organic alternative to improve plant growth, enhance soil fertility, and reduce soil salinity. The effectiveness of this alternative was evaluated through comparison with three types of fertilizers: inorganic chemical fertilizers, organic fertilizer derived from cattle manure, and a marine-based organic product extracted from shells and mollusks. The study relied on the collection and analysis of data related to germination rates, growth performance, plant health, and the impact of each fertilizer type on soil properties. The results indicated that chemical fertilizers, despite their rapid effectiveness in promoting germination, contribute to soil depletion and increased salinity when misused. Although animal-based organic fertilizers improved the physical properties of the soil, they were associated with environmentally harmful gaseous emissions. In contrast, the organic product derived from green mussel shells demonstrated promising results, including enrichment of the soil with calcium and essential minerals, replacement of sodium ions with calcium—thereby contributing to salinity reduction—improved root stabilization and fruit set, as well as reduced negative environmental impacts and sustainable utilization of marine resources. The study concluded that the use of marine shells represents an effective and sustainable agricultural option for addressing soil salinity issues and enhancing plant productivity, while promoting the utilization of local marine resources in the Sultanate of Oman. Furthermore, an innovative formulation was developed by combining marine shell powder with decomposed leaf residues, which yielded notable improvements in reducing soil salinity and enhancing the growth of fruit-bearing plants. These findings highlight the potential for practical application of this approach within sustainable agricultural systems.