In recent decades, intense human activities and increased maritime transportation triggered heavy pressure on the Israeli coastal ecosystem and, meanwhile, the eastern Mediterranean experienced the highest temperature values. With the assumption that both kinds of anthropogenic drivers could alter the benthic taxocenosis, a monitoring survey covering a period ranging from 2010 to 2017 was addressed to assess changes in the macrozoobenthos on spatial and temporal scales. The present study focused on the crustacean amphipod fauna collected on the soft bottom littoral area. Twenty-five species and taxa (genus level) were detected under the temporal survey in the same stations, located along a north-south axis, from the northernmost Haifa Bay to the southern area. The dataset showed a temporally stable assemblage of the most common species. Seven species showed the greatest abundance and a constant presence: the Levantine endemic Cheiriphotis mediterranea; the Mediterranean endemic Megaluropus massiliensis; the NE-Atlantic–Mediterranean Bathyporeia guilliamsoniana and Perioculodes longimanus; and the widely distributed Photis longicaudata and Urothoe grimaldii. In addition, an alien species was recorded, the circumtropical aorid Grandidierella bonnieroides which resulted naturalized. Differently, the spatial dataset discriminated two geographical regions, the northernmost Haifa Bay and the remaining Southern Israeli Coast, based on the different substratum granulometry. On the whole, the Israeli assemblage showed a low diversity composed of dominant species strictly associated with the features of the sediment and characterised by local abundance fluctuations. It is a pattern that provides baseline knowledge for successive monitoring years and contributes to implementing the knowledge of the ecological traits of amphipod fauna.