Remote underwater video systems (RUVS) are increasingly used in scientific studies to monitor marine ecosystems. RUVS can be deployed baited (BRUVS) or unbaited (UBRUVS) and allow for an estimation of the MaxN metric, a relative measure of species abundance. Recording species MaxN in a variety of marine habitats provides associations between species abundance and habitat type, known as ‘species-habitat relationships’. However, the introduction of bait in BRUVS could obscure such relationships by inadvertently attracting fish from neighbouring habitats. Here, we investigate the species-habitat relationships of seven temperate marine species: Atlantic cod (Gadus morhua), right-eyed flatfish (Pleuronectinae spp.), Atlantic herring (Clupea harengus), whiting (Merlangius merlangus), goldsinny wrasse (Ctenolabrus rupestris), two-spotted goby (Gobiusculus flavescens) and shore crab (Carcinus maenas) as revealed by BRUVS and UBRUVS. Video systems were deployed in coastal areas in the Western Baltic, with a cobble coverage ranging from 0% to 100%. Results show that all focal species responded to changes in cobble coverage, highlighting the importance of benthic habitat for a range of animals including benthopelagic species. Specifically, mean abundances of goldsinny wrasse and two-spotted goby were positively associated with cobble coverage, whilst right-eyed flatfish, herring, whiting and shore crab showed a negative association. Atlantic cod was found to be most abundant at intermediate cobble coverage between 65 and 70%, showing a unimodal trend with the mean abundance decreasing again at higher coverage. The relationships suggest that anthropogenic activities modifying benthic habitats, including extraction of material from the seabed and bottom trawling, likely change abundances of a range of marine species. Our comparative analysis suggests that both BRUVS and UBRUVS can identify previously documented species-habitat relationships. However, BRUVS demonstrated some superiority by confirming documented relationships for Atlantic cod and whiting, whilst UBRUVS failed to record any patterns for those species. Our data highlight the ability of BRUVS to identify changes in abundance across different habitats for a variety of species. Although the bait plume serves to attract organisms to the field of view, current results suggest that the use of BRUVS does not obscure species-habitat relationships in patchy coastal habitats. Therefore, future studies examining the importance of different marine areas may benefit from using BRUVS to quantify relationships between habitat variables and species abundance. Developing a better understanding of such relationships will be crucial in ensuring adequate management and protection of ecologically important marine habitats.