An important aspect of environmental studies on freshwater ecology is the mapping of benthic habitats, which are important for primary production as well as serving as a shelter for organisms. Therefore, accurate sampling methods must exist for the evaluation of freshwater ecosystems, especially the benthic habitat. Here we compare the operation and efficiency of a modified Surber sampler with a constructed manual suction pump system. We used these systems for sampling the variable areas encountered within Silfra, a freshwater fissure in Þingvellir National Park, southwest Iceland. Each method was used to take five repetitions of samples at two different depths. The stations chosen covered submerged vertical walls and a hard bottom, inhabiting a variety of invertebrate organisms. Our results show that the manual suction pump system collected a greater number of both individuals and taxa at the two depths in question. It´s use also proved more practical and reliable for the various conditions encountered in the fissure.