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Bahia Concepcion is a coastal bay, in the Gulf of California, Mexico, free of significant human impacts. Summer rainfall influences the physical and chemical characteristics of this bay. Salinity and nutrient data collected before and after a tropical rainstorm were evaluated with a mass-balance model to show that, after rainfall, water residence time is reduced, and that moderate nitrogen gain and phosphorus excess occurs. Hydraulic balance is not re-established 12 days after the rain, when nitrogen flux approximates pre-rainfall conditions, while phosphorus flux did not show a return to pre-rainfall conditions. Coastal management strategies for semi-enclosed deep water bodies in and zones should include transient regulations to cope with natural disturbing pulses. (c) 2005 Elsevier Ltd. All rights reserved.