Reconstructing ocean surface nutrients from sparse observations is critical for understanding long-term biogeochemical cycles. Most prior work focuses on reconstructing atmospheric fields and treats the reconstruction problem as image inpainting, assuming smooth, single-scale dynamics. In contrast, nutrient transport follows advection–diffusion dynamics under nonstationary, multiscale ocean flow. This mismatch leads to instability, as small errors in unresolved eddies can propagate through time and distort nutrient predictions. To address this, we introduce NUTS, a two-scale reconstruction model that decouples large-scale transport and mesoscale variability. The homogenized solver captures stable, coarse-scale advection under filtered flow. A refinement module then restores mesoscale detail conditioned on the residual eddy field. NUTS is stable, interpretable, and robust to mesoscale perturbations, with theoretical guarantees from homogenization theory. NUTS outperforms all data-driven baselines in global reconstruction and achieves site-wise accuracy comparable to numerical models. On real observations, NUTS reduces NRMSE by 79.9% for phosphate and 19.3% for nitrate over the best baseline. Ablation studies validate the effectiveness of each module.