•Spatial and temporal distribution of currently used pesticides in the Guadalquivir River Basin.•Organophosphorus>triazines>carbamates are the most commonly detected.•Transformation products were found at higher concentrations than parent pesticides.•WWTP are an important source of pesticide to the environment.•Low accumulation levels in sediments and biota. The occurrence of 50 currently used pesticides and their transformation products in surface and waste waters, sediment and fish in the Guadalquivir River Basin was determined in 2010 and 2011. After selective sample extraction, pesticides were identified and quantified by liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS). The contamination profile in water and sediments is marked by the presence of organophosphorus and triazines. Transformation products were even at higher concentrations than parent pesticides. A wider range of pesticides was present in water than in sediments but none of them were detected in fish. The mean concentrations ranged from 0.2 to 13.0ng/L in water and from 0.1 to 13.2ng/g d.w. in sediment. The spatial distribution of most pesticides was consistent with the agricultural activities of the area or their urban applications. The waste water treatment plant effluents that impact the river are minor sources for few pesticides but for most of them run-off would be the most important contribution. The temporal distribution showed differences between both sampling campaigns related to the river flow. The low-flow produced a pesticide concentration effect, generating higher levels in water and accumulation in sediments. This forecasts a hazard in future scenarios if the current situation of the climate change and water scarcity evolves to more critical conditions highlighting the need of these monitoring studies.