Monitoring of pesticide residues in water and sediments was conducted as a basis for subsequent ecotoxicological risk assessment for the shallow eutrophic Lake Pamvotis, northwestern Greece. During a one-year study period, atrazine, desethylatrazine (DEA), simazine, diazinon, malathion, oxamyl, carbofuran, and ethion were detected in water and atrazine, desethylatrazine, diazinon, and s-ethyl dipropylthiocarbamate (EPTC) in sediments, all at ppb concentration level. Temporal variation in pesticide concentrations was observed. Highest residue levels for most pesticides in both water and sediment matrices occurred in the May to July period with the exception of atrazine and DEA, which show highest levels in water during the September to November period. The ecological risk associated with pesticide contamination was assessed using two different methods: The toxic unit method, which provides a first indication of the relative contribution of detected pesticides to the total toxicity and a probabilistic approach, and the inverse method of Van Straalen and Denneman, which is used to quantify the ecological risk. The maximum percentage of the ecological risk was 10.3 and 51.8% for water and 17.2 and 70.6% for sediment, based on acute and chronic level, respectively. These results show that pesticides exert a significant pressure on the aquatic system of Lake Pamvotis, especially for the chronic-effect level. Simple quotient methods should be coupled with higher-tier risk assessment, especially if restoration activities on lake ecosystems are to be undertaken for sustainable development.