Intensive shrimp aquaculture has increased by about 20% per year during the last decade along the semi-arid NE coast of Brazil due to the optimal climate and environmental setting. Emissions of N and P from this activity to 16 estuaries along the coast of Ceará and Rio Grande do Norte states, NE Brazil, where about 80% of the shrimp farming area of the country is located, showed that intensive shrimp farming presents average emission factors for N and P ranging from 6 to 664 kg.km-2 .yr-1 and from 0.4 to 77 kg.km- 2 .yr-1 , respectively. These emission factors resulted in total annual emissions of 9 to 485 t.yr-1 and 0.7 to 35 t.yr-1 , for N and P respectively. Larger loads occurred at the Jaguaribe River (Ceará State) and the Açu River (Rio Grande do Norte State). Intensive shrimp farming is the major relative contributor of N to the Jaguaribe (CE) (41%) and Açu (RN) (63%) basins. Also at the Guamaré basin (RN) it contributes with 26% of the total N load. Contribution of P from intensive shrimp farming is relatively small varying from <5% in most basins to a maximum contribution of 13% at the Açu basin (RN). Although the contribution of intensive shrimp farming relative to agriculture and husbandry is small in most of the studied areas, the location of farms adjacent to estuaries makes possible direct inputs to waters, while most other emissions go firstly to soils before eventually being transported to surface waters.