The impact of diffuse pollution in aquatic systems is of great concern due to the difficult to measure and regulate it. As part of an ecological risk assessment (ERA), this study aims to use a whole sample toxicity assessment to evaluate the toxicity of water and sediment from Lake Vela, a lake that has been exposed to diffuse pollution. In this way, standard (algae: Pseudokirchneriella subcapitata; cladoceran: Daphnia magna) and local species (algae: Aphanizomenon flos-aquae; cladoceran: Daphnia longispina) were exposed to surface water, and sediment elutriates were collected seasonally from two sites at Lake Vela: one near the east bank (ES), surrounded by agricultural lands; and the other near the west bank (WS), surrounded by a forest. The results confirmed the seasonal contamination of both environmental compartments by pesticides, including organochlorine pesticides, and the presence of high concentrations of nutrients. Although both sites were contaminated, higher levels of pesticides and nutrients were detected in ES, particularly in the sediments. Bioassays showed that water samples (100% concentration) collected in summer and autumn significantly affected the growth rate of P. subcapitata, which could be attributed to the presence of pesticides. Likewise, they revealed an apparent toxicity of elutriates for P. subcapitata and for both daphnids, in summer and autumn. In fact, although pesticides were not detected in elutriates, high levels of un-ionized ammonia were recorded, which is considered highly toxic to aquatic life. By comparing the several species, P. subcapitata was revealed to be the most sensitive one, followed by the daphnids, and then by A. flos-aquae. Results obtained in this study underlined the importance of whole samples toxicity assessment for characterizing the ecological effects of complex mixtures from diffuse inputs, in the ERA processes.