The flow of chemical materials along spatial elements is a fundamental aspect of landscape ecology. The research renders indicators for water pollution, which are utile for functional water management and land use planning. Ecologists identify mechanisms of nutrients transfer and mitigate their environmental impacts using freshwater wetlands and riparian buffers. In order to estimate the N (nitrogen) and P (phosphorus) loss risk, current research combines indicators into index models. The objective of this work was to review the factors of transport from upland source areas to surface water as N and P indicators, and to report on the magnitudes of N and P fluxes in agricultural landscapes under temperate climate. We reviewed the ISI Web of Science for recent developments on N and P transport factors and nutrient index models, and we suggested how to improve these schemes. We presented conceptual diagrams of N and P transport. Catchment-scale index models use factors of contributing distance, connectivity, soil properties, and erosion as indicators. P losses are mainly dependent on overland flow conduits and barriers, whereas subsurface flows control N more. Riparian vegetation accumulates great N and P amounts, while it is usually just a temporary sink. Riparian soil is a smaller but a more permanent store, whereas it may turn to a nutrient sink, too, when saturated. Anaerobic soil microbes denitrify somewhat less N, while this process is irreversible, and therefore equally crucial. In spite of this, most nutrient index models do not consider wetlands and riparian buffers. Hence we suggest to include the removal capacity of the riparian buffer zone in both catchment N and P index models. In general, we propose a landscape framework, which considers upland source areas, transit, and hydric riparian landscape elements as a single system.