In studies on the biochemical compounds in phytoplankton, water samples generally are (pre-) filtered to retain the organisms for extraction. Such filters can be used for further investigations in microscopic or chromatographic (for example High-Performance-Liquid-Chromatography, HPLC) methods, while the filtrates can be used for nutrient or fluorometric measurements as well as for microscopic examinations. Which filter is chosen for a study often depends on its pore size, the costs and, in particular for HPLC measurements, on its chemical compatibility. In our study we compared the chlorophyll-a retention on the filters by HPLC as well as the fluorescence before and after filtration, and nutrient content of the filtrates. The filters we tested were of different material and with various pore sizes. Although Whatman GF/C and GF/F filters are preferred in phytoplankton studies, we found that the Nylon Membrane filter of 0.2 μm pore size provided the most consistent results in chlorophyll-a retention and the one of 0.45 μm pore size in nutrient investigations. © 2007 Elsevier B.V. All rights reserved.