Fisheries constitute a major threat to marine mammals globally. To evaluate the impact of small-scale fisheries (SSF) on regional under-studied marine mammal populations, we tested a novel and cost-effective approach at three data-limited locations of the central and eastern Mediterranean Sea. Using off-the-shelf GPS loggers to track SSF activities and systematic surveys to map the distribution of marine mammals, we assessed the probability of co-occurrence between SSF and marine mammals by reporting areas of spatial overlap. Spatial overlap between SSF and the core zones of marine mammal distribution (ranging between 21.85–35.4%) was observed in all three locations, indicating potential interaction hotspots. The probability of co-occurrence in those areas varied from 0.5–2.9% depending on the species. The resulting overlap between fishing activity and marine mammals may pose a threat in both directions: higher risk of species entanglement and economic burden on fishers due to gear damage. Despite the spatial and temporal limitations of this pilot study, the proposed approach can provide baseline information on SSF-marine mammal co-occurrence, particularly in financially limited regions. If applied on a larger scale, our method may be used to inform future conservation actions with the aim to reduce pressure on key populations.