This data set contains information about near-surface (about 10 m depth) gelatinous zooplankton assemblages and their seasonal changes from two neighbouring Northwestern Icelandic fjords, which were studied from April to September 2008. At five stations, horizontal Bongo net (mesh size: 500 µm, mouth opening: 0.3 m²) tows were performed regularly with a small motor boat at a towing speed of about 3 kn. In total, 12235 specimens of 14 species (ten hydromedusae, two scyphomedusae, one ctenophore) were collected. The total abundance of gelatinous zooplankton increased from April to June, while scyphomedusa and ctenophore abundances decreased towards September.