It is presented in this work a new methodology to harvest fresh water microalgae cultures by extracting the culture medium with superabsorbent polymers (SAPs). The microalgae Chlamydomonas reinhardtii were grown in the Sueoka culture medium, harvested with polyacrylic SAPs and re-suspended in the culture medium tris-acetate-potassium without sulfur (TAP-S) to generate hydrogen (H2) under anoxic conditions. The H2 production as an alternative fuel is relevant since this gas has high-energy recovery without involving carbon. Before microalgae harvesting, a number of range diameters (1–7 mm) for SAPs spherical particles were tested, and the initial rate (V0) and the maximal capacity (Qmax) were determined for the Sueoka medium absorption. The SAP particles with the diameter range 2.0–2.5 mm performed the best and these were employed for the rest of the experiments. The Sueoka medium has a high salt content and the effect of the ionic strength was also studied for different medium concentrations (0–400%). The SAPs were reused in consecutive absorption/desorption cycles, maintaining their absorption capacity. Although the Sueoka medium reduces the SAPs absorption capacity to 40% compared with deionized water, the use of SAPs was very significant for the desulfurization process of C. reihardtii. The presence of C. reinhardtii at different concentrations does not affect the absorption capacity of the Sueoka culture medium by the SAPs. In order to reduce the time of the process, an increase of the SAPs concentration was tested, being 20 g of SAP per liter of medium, a condition to harvest the microalgae culture in 4 h. There were no evident cell ruptures during the harvesting process and the cells remained alive. Finally, the harvested biomass was re-suspended in TAP-S medium and kept under anaerobic conditions and illumination to produce H2 that was monitored by a PEM fuel cell. The use of SAPs for microalgae harvesting is a feasible non-invasive procedure to obtain high concentrations of functional biomass at low cost; it offers an attractive alternative due to its versatility and simplicity. Biotechnol. Bioeng. 2013;110: 3227–3234. © 2013 Wiley Periodicals, Inc.