Ocean-based carbon dioxide removal (CDR) strategies are increasingly explored to enhance the ocean’s natural capacity to absorb atmospheric CO₂ and mitigate climate change. Among the proposed approaches, ocean fertilization aims to stimulate phytoplankton productivity and, where export is achieved, potentially strengthen the biological carbon pump. However, conventional fertilization techniques involving direct nutrient addition often suffer from rapid nutrient dilution, short residence times in the euphotic zone, and uncertain ecological outcomes. Importantly, short-term biological carbon uptake in surface waters must be distinguished from verified long-term carbon sequestration. In this study, we evaluate a biodegradable nutrient-delivery system—eco-engineered buoyant flakes—designed to release bioavailable micronutrients and silicate within surface waters. Microcosm and mesocosm experiments conducted in the eastern Arabian Sea assessed whether these flakes enhance nutrient availability and produce detectable biological and microbial responses under oligotrophic conditions. Flake additions increased silicate and bioavailable iron concentrations and were associated with modest changes in chlorophyll a, fucoxanthin, phytoplankton abundance, and microbial community composition. These biological responses coincided with increases in pH, reductions in pCO₂, and modest increases in total organic carbon, indicating short-term surface-water carbon uptake rather than verified carbon sequestration. Nitrogen limitation, grazing pressure, turbulence, and the short experimental duration constrained bloom magnitude. This proof-of-concept study therefore demonstrates nutrient-release potential and detectable ecosystem responses, while longer-term, replicated studies are required to quantify carbon export efficiency, ecological impacts, and the true relevance of the proposed CDR method.