An automated system was developed for analysis of non-polar and polar ionisable compounds at trace levels in natural water. Sample work-up was performed in a flow system using two parallel membrane extraction units. This system was connected on-line to a reversed-phase HPLC system for final determination. One of the membrane units was used for supported liquid membrane (SLM) extraction, which is suitable for ionisable or permanently charged compounds. The other unit was used for microporous membrane liquid-liquid extraction (MMLLE) suitable for uncharged compounds. The fungicide thiophanate methyl and its polar metabolites carbendazim and 2-aminobenzimidazole were used as model compounds. The whole system was controlled by means of four syringe pumps. While extracting one part of the sample using the SLM technique. the extract from the MMLLE extraction was analysed and vice versa. This gave a total analysis time of 63 min for each sample resulting in a sample throughput of 22 samples per 24 h.