The spatial and seasonal distributions of current-use pesticides (CUPs), including triazines, organophosphorus pesticides, and tributylphosphate, were characterized in surface sediments from the Mar Menor lagoon during 2009 and 2010. The impact of two flash flood events on the input of CUPs and their distribution in the lagoon were also assessed. The total (dissolved + sorbed phase) input of CUPs in the two flash floods through the El Albujón watercourse into the lagoon was estimated at 38.9 kg, of which 9.9 kg corresponded to organophosphorus pesticides and 5.5 kg to triazines. CUP distribution onto sediments was not homogeneous in the lagoon due to the different contaminant sources, sediment types, and the physicochemical and hydrodynamic conditions of the Mar Menor lagoon. Thirteen CUPs were detected in 2009 and 19 in 2010, including mainly herbicides, insecticides, and the additive tributylphosphate. Mean CUP concentrations in the lagoon were generally below 20 ng g-1, except for chlorpyrifos and tributylphosphate in 2010. The highest concentrations were detected in depositional areas of the lagoon, in the area of influence of the El Albujón watercourse and other wadis with groundwater contributions such as El Mirador (north) and Los Alcázares (east) and that of marine water from El Estacio channel. In fact, the maximum concentration was detected close to El Albujón watercourse (chlorpyrifos, 102.8 ng g-1 dry weight). Four herbicides, two insecticides, two fungicides, and tributylphosphate showed a risk quotient higher than 1, with that for chlorpyrifos ranging from 96 to 35,200 after flash flood events.