The loss of biodiversity is recognised on a global scale and also in the anthropogenic landscapes used for agriculture, now covering almost 50% of the global terrestrial land surface. In agriculture pesticides, biologically active chemicals are deliberately distributed to control pests, disease and weeds in the cropped areas. The quantification of remaining semi-naturals structures such as field margins and hedges is a prerequisite to understand the impact of pesticides on biodiversity, since these structures represent habitats for many organisms in agricultural landscapes. The presence of organisms in these habitats and crops is required to obtain an estimate of their potential pesticide exposure. In this text I provide studies on animal groups so far not addressed in risk assessment procedures for the regulation of pesticides such as amphibians, moths and bats. For all groups it becomes apparent that they are present in agricultural landscapes and potentially coincide with pesticide applications indicating a risk. Risk quantification also requires data on the sensitivity of organisms and here data for plants, amphibians and bees are presented. Effects translating to community level were studied for herbicide, insecticide and fertiliser effects in a natural system. After three years the treatments resulted in simplified plant communities with lower species numbers and a reduction in flowering plants. This reduction of flowers is used as an example for an indirect effect and was especially obvious for the effect of an herbicide on the common buttercup. Sublethal herbicide effects for a plant translated in an impact on feeding caterpillars, indicating a reduction in food quality. Insecticide inputs realistic for field margins also reduced moth pollination of white champion flowers by 30%. These indirect effects by distortions of food web characteristics are playing a critical role to understand declines in organism groups, however so far are not accounted for in pesticide risk assessment schemes. The current intense use of pesticides in agriculture and their inherent toxicity may lead to a chemical landscape fragmentation, where populations may not be connected anymore. Source-sink dynamics are important ecological processes and as a final result not only population size but also genetic population structure might be affected. Including potential pesticide impacts as costs in a model for amphibians migrating to breeding ponds in vineyards in Rhineland-Palatinate indicated the isolation of investigated populations. A first validation by analyzing the population structure of the European common frog confirmed the model prediction for some sites. For the regulation of pesticides in Europe a risk assessment is required and for the organisms of the terrestrial habitat a multitude of guidance documents is in place or is recently developed or improved. The results of the presented research indicate that wild plants and especially their reproductive flower stage are highly sensitive and risks are underestimated. Population recovery of arthropods needs a reevaluation at landscape scale and the addition of amphibian risk assessment in regulation procedures is suggested. However, developing or adopting risk assessment procedures and test systems is a time consuming task and therefore the establishment of risk management options is a pragmatic alternative with immediate effects. Artificial wetlands in the agricultural landscape proved to be important foraging sites for bats and their creation could mitigate negative pesticide effects. The integration of direct and indirect effects in a risk assessment scheme for all organism groups addressing also landscape scale and pesticide mixtures requires a long developing time. The establishment of model landscapes where management options and integrated pest management are applied on a larger scale would allow us to study pesticide effects in a realistic scenario and to develop an approach for the agriculture of the future.