Magnetic nanomaterials (MNMs), particularly iron oxide-based nanoparticles, are demonstrating increasing potential as multifunctional agents in agriculture, with roles including use as nanofertilizers, stress modulators, and tools for environmental remediation. The unique physicochemical properties of these particles, including superparamagnetism, a high surface area, and tunable surface chemistry, enable efficient uptake, translocation, and integration into metabolic pathways within plants. Such remarkable properties have extended the uses of MNMs in diverse fields. In the present chapter, we have focused on their uses in agricultural and biological sciences. We have focused on the physiological and molecular responses of plants to MNM exposure. In this regard, the changes in germination, growth, photosynthesis, water relations, oxidative balance, and stress signaling were discussed. Concerning biochemical and molecular levels, MNMs were found to modulate antioxidant enzyme activities, secondary metabolite biosynthesis, gene expression, and signaling cascades such as MAPK and calcium-mediated pathways, often in a dose- and species-dependent manner. In the frame of hormetic approach, it was noted that while low concentrations enhance nutrient use efficiency and stress resilience, excessive exposure can disrupt redox homeostasis, damage cellular structures, and alter transcriptomic profiles. Regarding the ecotoxicological concerns, environmental fate studies reveal that MNMs undergo aggregation, dissolution, and interactions with soil and aquatic biota, raising concerns of bioaccumulation, ecotoxicity, and disruption of microbial consortia. The dual role of MNMs—as both growth-promoting agents and potential toxicants—underscores the need for standardized testing, long-term field trials, and eco-friendly synthesis approaches. Taking all the findings of the literature into account, this chapter provides insights into the safe, sustainable, and climate-resilient integration of MNMs into modern agriculture.