Natural toxins such as phytotoxins and mycotoxins have been studied in food and feed for decades, but little attention has yet been paid to their occurrence in the environment. Because of increasing awareness of the presence and potential relevance of micropollutants in the environment, phytotoxins and mycotoxins should be considered and investigated as part of the chemical cocktail in natural samples. Here, we compile chemical analytical methods to determine important phytotoxins (i.e. phenolic acids, quinones, benzoxazinones, terpenoids, glycoalkaloids, glucosinolates, isothiocyanates, phytosterols, flavonoids, coumestans, lignans, and chalcones) and mycotoxins (i.e. resorcyclic acid lactones, trichothecenes, fumonisins, and aflatoxins) in environmentally relevant matrices such as surface water, waste water-treatment plant influent and effluent, soil, sediment, manure, and sewage sludge. The main problems encountered in many of the reviewed methods were the frequent unavailability of suitable internal standards (especially isotope-labelled analogues) and often absent or fragmentary method optimization and validation.