The cultivation of rice (Oriza sativa L.) under Mediterranean conditions regularly requires the use of treated wastewater due to shortage of freshwater. As a consequence, the intensification of rice production to supply the uprising demand of grain could break the stability between agriculture and environment. In this work, we studied the occurrence and distribution of pyrethroids in surface water and groundwater collected during two periods (flooding and dry soil conditions) in paddy fields located in the Spanish Mediterranean coast. Pyrethroids were detected at concentrations ranging from 14 to 1450 ng L−1 in surface water and from 6 to 833 ng L−1 in groundwater. The results obtained were evaluated statistically using principal component analysis, and differences between both sampling campaigns were found, with lower concentrations of the target compounds during the flooding sampling event. Moreover, a geographic information system program was used to represent a model distribution of the obtained results, showing wastewater treatment plants as the main sources of contamination and the decrease of pyrethroids during flooding condition when water flows over the paddy fields. The impact of these compounds on water quality was discussed. © 2016, The International Society of Paddy and Water Environment Engineering and Springer Japan.