This chapter provides insights into the difficulties and challenges of performing risk evaluations of agrochemicals. It is a critical review of the current methodologies used in ecological risk assessment of these chemicals, not their risks to humans. After an introduction to the topic, the current framework for ecological risk assessment is outlined. Two types of assessments are typically carried out depending on the purpose: i) regulatory assessments for registration of a chemical product; and ii) ecological assessments, for the protection of both terrestrial and aquatic ecosystems, which are usually site-specific. Although the general framework is well established, the methodologies used in each of the steps of the assessment are fraught with a number of shortcomings. Notwithstanding the subjectivity implicit in the evaluation of risks, there is scepticism in scientific circles about the appropriateness of the current methodologies because, after so many years of evaluations, we are still incapable of foreseeing the negative consequences that some agrochemicals have in the environment. A critical appraisal of such methodologies is imperative if we are to improve the current assessment process and fix the problems we face today. The chapter reviews first the toxicity assessment methods, pointing to the gaps in knowledge about this essential part of the process and suggesting avenues for further improvement. Deficiencies in the current regulations regarding toxicity testing are discussed, in particular the effect of the time factor on toxicity and the issue of complex mixtures.