This paper analyzes inter-annual (1993-2008) and intra-annual (2006-2008) flooding patterns in the unregulated San Pedro River, based on digital analysis of two Landsat satellite imagery series and ancillary rainfall and discharge data, to describe variations in the natural pulse. The long-term pattern, over a period of 16 years, showed considerable fluctuations, with a maximum flood extent (FE) of approximately 200 km2, while the observed average was 57.8 km2 over the entire period, around 24 km2 the dry season and more than 90 km2 in the rainy season. The seasonal variation, analy zed using 29 quasi-monthly images recorded from 2006 to 2008, displayed FE peaks in the rainy season (July to October) with variations in time and extent that were not directly related to rainfall but instead were related to river discharge, Q, (FE = y0 + a(1-0.9983Q); R2 = 0.91). We used the above exponential model with monthly average river discharge data (1944-2008) and the proposed regulated volume of discharge from governmental plans to construct a dam on the San Pedro River. We found that the natural ecosystem will be altered by increasing the inundation in the dry season and reducing it in the rainy season. This change will have consequences in coastal wetlands and aquatic biota adapted to historical conditions, with consequences for the production of aquatic organisms and for ecosystem services.