Alkylphenolic compounds derived from microbial degradation of non-ionic surfactants became a major focus of environmental research in the early 1980s. More toxic than the parent compounds and weakly oestrogenic, certain metabolites of nonylphenol polyethoxylate (NPnEO) surfactants, especially nonylphenol (NP), raised sustained concern over the risk they pose to the environment and triggered legal measures as well as partly voluntary actions by the manufacturing industry. Continuous progress in the development of analytical techniques is crucial to understand how these alkylphenolic compounds behave in wastewater treatment, the aquatic environment and in laboratory experiments. Measured concentrations and mass flows of phenolic endocrine disruptors, particularly nonylphenolic compounds, bisphenol A and parabens in municipal wastewater effluents and in the Glatt River, Switzerland, show that rain events leading to discharges of untreated wastewater into rivers have a great impact on the riverine mass flows of contaminants. Biotransformation experiments in our laboratory with nonylphenoxyacetic acid and individual NP isomers enabled the elucidation of degradation pathways of these compounds. The finding that nonylphenoxyacetic acid is metabolized via NP further underscores the role of NP as the most relevant metabolite in the degradation of NPnEO. Several Sphingomonadaceae bacterial strains were found to degrade α-quaternary 4-NP isomers by an ipso-substitution mechanism, and to use only the aromatic part of the molecule. These reactions turned out to be isomer specific, meaning that rate and extent of transformation depend on constitution, and possibly also on the absolute configuration of the alkyl side chain of a specific isomer. The observation that NP isomers with distinct oestrogenic activities are differentially degraded has significant implications for risk assessment.