A study was conducted on the occurrence of 50 pesticides in water and sediments of Turia and Júcar Rivers (Valencian Community, Eastern Spain) for a period of two consecutive years each, 2010/2011 and 2012/2013, respectively to assess the contribution of agriculture and urban activities on pesticide pollution. The results showed that mean concentrations of pesticides ranged from <. LOQ up to 200. ng/L. Chlorpyrifos was the most frequent pesticide whereas imazalil, thiabendazole, tolclofos methyl, ethion and carbofuran were those found at higher concentrations. Ubiquitous pesticides are those with long half-lives. The most polluted parts of the rivers were the headwaters and the mouth, which could be related to the agricultural practices and rainfall. Contrarily, in the abrupt part of the rivers of difficult access the contamination is low. Other quality parameters monitored in this study also corroborate the worst water quality in the alluvial plains that coincides with higher anthropic pressure. The temporal variations also indicated a strong relation of pesticide concentrations with hydrology, the higher the river flow, the higher number and frequency of pesticides but at lower concentrations. On the contrary, at lower river flows higher pesticide concentrations were detected. The risk assessment for aquatic biota pointed out that organophosphorus and fungicides are a threat to fish and daphnia and herbicides and fungicides are hazards for algae. Thus, the strict control of pesticide concentrations is important to preserve the aquatic ecosystems health.