Iceland has an abundance of fissures that are parallel to the Mid-Atlantic ridge where bedrock cracks as a result of continental rifting. Some fissures penetrate the aquifer and expose the groundwater within the bedrock, becoming springs. As such, groundwater fissures have uniform and constant physical and chemical environment but they can differ greatly in morphology. In addition, there is often great variation in depth within fissures and substrate types contrast between vertical rock wall and more heterogenous horizontal bottom. The variation in morphological environment may create dissimilar habitats with unique characteristics and/or influence distribution of resources. Our objective was to study macrozoobenthos communities in cold groundwater fissures in Iceland in relation to physical habitat by comparing invertebrate diversity and density both between fissures with different morphological characteristics as well as between substrate types and depths within fissures. Samples were collected in two fissures in SW Iceland, Silfra and Flosagjá. Assemblages were similar between fissures except for higher densities of cladocerans in Flosagjá fissure. Within fissures, there was significant difference in Shannon diversity between substrate types in Flosgjá and ostracods were found in significantly higher densities on bottom. The distribution of all other taxa groups was homogenous in both fissures regardless of depth gradient and substrate. Invertebrates were found to be living within and around a biofilm that covered the entire substrate. These biofilm mats are made from Cyanobacteria and benthic diatoms, which are successful under low light conditions and may minimize any effect of the heterogeneous habitat creating a uniform and suitable microhabitat for invertebrates regardless of depth and substrate type.