The spatial structure of seagrass landscapes is typically ascribed to the direct influence of physical factors such as hydrodynamics, light, and sediment transport. We studied regularly interspaced banded patterns, formed by elongated patches of seagrass, in a small-scale intertidal ecosystem. We investigated (1) whether the observed spatial patterns may arise from feedback interactions between seagrass and its abiotic environment and (2) whether changes in abiotic conditions may lead to predictable changes in these spatial patterns. Field measurements, experiments, and a spatially explicit computer model identified a “scale-dependent feedback” (a mechanism for spatial self-organization) as a possible cause for the banded patterns. Increased protection from uprooting by improved anchoring with increasing seagrass density caused a local positive feedback. Sediment erosion around seagrass shoots increased with distance through the seagrass bands, hence causing a long-range negative feedback. Measurements across the depth gradient of the intertidal, together with model simulations, demonstrated that seagrass cover and mean patch size were predictably influenced by additional external stress caused by light limitation and desiccation. Thus, our study provides direct empirical evidence for a consistent response of spatial self-organized patterns to changing abiotic conditions, suggesting a potential use for self-organized spatial patterns as stress indicators in ecosystems.