Deep-sea offshore northwestern Cuba is the less studied zone of the Gulf of Mexico (GoM). Our study aimed to set an environmental baseline and investigate a potential west-east gradient of sediment properties and nematode diversity along the northwestern Cuba. Sediments were collected by multicorer at nine sites in the insular slope between 974 and 1682 m depth. Sediment texture and composition showed a west-east gradient caused likely by narrowing of shelf width and increasing of downslope transport of terrigenous material. We found clear signatures of heavy metal pollution likely derived from Havana City but also from open-sky mining (Castellanos mining complex) and port dredging operations (Mariel). Nematode assemblages were dominated by the deep-sea genera: Acantholaimus, Metadasynemella, Desmodorella, Cervonema, Daptonema, Halalaimus, and Pselionema. α-diversity was about 20–50 genera and γ-diversity of about 100 genera. The β-diversity was substantial likely because small-scale patchiness of resources and heavy metals stress that increased assemblage variability. Individual weight decreased with depth indicating food-supply limitation in the deep sea; also, heavy metals were negatively correlated with weight suggesting deleterious effects on the growing. Our findings indicate that heavy metal pollution has reached deep-sea sediments and corroborate the long-range effects of anthropogenic activities on deep sea. Taxonomic diversity and biological traits (life strategy and trophic composition) constituted a powerful bioindicator of benthic health and benchmark for future potential disturbances in the region. Northwestern Cuba slope is still an understudied portion of the GoM and more research is needed to fully understand its biodiversity and biogeochemical patterns.