Small pelagic fish are key components of productive coastal ecosystems, yet their migration ecology remains poorly understood, causing challenges for management. We applied stable carbon and nitrogen isotope (δ13C and δ15N) analyses of eye lenses to investigate movements of European anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) around the Iberian Peninsula. Muscle isotopes showed strong spatial heterogeneity, largely consistent between species and reflecting differences in baseline values. Eye lens centres of small anchovy, and to a lesser extent sardine, showed clear geographic variation: higher δ15N off the Atlantic south coast, lowest δ15N in the Alboran Sea, and lower δ13C off the west coast. These patterns persisted across years and fish sizes in anchovy, with only minor outliers, suggesting limited cross regional migration. An exception was the overlap between west coast and Cantabrian Sea values, consistent with connectivity supported by cohort tracking. In contrast, sardine isotopes from the west and south coasts converged into a unimodal distribution with growth, indicating frequent exchange between these regions. These findings support recent revision of stock limits that separate south and west coast anchovy stocks, but they question the current assumption of separation between western and northern Iberian anchovy stocks. Eye lens isotopes provide a powerful complementary tool to resolve nursery origin and connectivity, offering new opportunities for fisheries management in shorter time scales than molecular techniques, which is paramount to be able to cope with rapid changes of fish distribution due to climate change, and for spatially explicit management.