A two-year study was carried out in the lower part of the Palmones River to describe the role of a small dam controlling the nutrient fluxes to the estuary. Results showed an important spatial heterogeneity in the nutrient content and water properties of lowland catchment due to the dammed water and the effluents of a sewage treatment work. Taking into account the values of hydraulic retention time, the dam could be considered as an optimally dimensioned pre-dam. Therefore, it removed on average more than 25 % of total phosphorus (TP) reaching during the dry season values of 55 %. Total nitrogen (TN) showed higher seasonal variability than TP, ranging between a removal of 79.8 % and an increase of 41.2 %. Palmones River exported 11.3 TonsP y-1 of TP and 72.1 TonsN y-1 of TN to the estuary showing important seasonal differences. Less than 10 % from the total amount of nutrient was exported during low flow conditions, while in three months with important flooding events, the percentage of total nitrogen exported reached 64.5 %.