This study was undertaken in view of the ever-increasing threat of marine pollution along Karachi coast and its possible danger to the coastal and marine environment. It is an effort to identify the biological threats zones due to water pollutants in the coastal environment of Karachi, Pakistan. Water samples were collected from various locations along the coastline of Karachi and analysed for physico‐chemical parameters. The overall coastline of Karachi can be considered as a threat zone for the lives associated with it because of higher levels of hexane extractable materials, conductivity, total dissolved solids, Co, Cu, Cd and As in water than the permissible limits suggested by World Health Organization/National Environmental Quality Standard, at each sampling site. Paradise Point and Kemari Harbour, particularly are found to be the highest biological threat zones because these sites contained highest concentrations of hexane extractable materials. The concentration of dissolved oxygen showed strong negative correlation (r = − 0.936) with hexane extractable materials concentration. Hawkes Bay and Sea view are another biological threats zones in terms of highest levels of conductivity, total dissolved solids, Cd, As, Fe, Cu, Co and Ni in water samples at these sites that can be lethal to the flora and fauna associated with it. The results suggested that immediate actions should be taken to control the marine pollution along the coastline of Karachi for the sustainability of coral reefs, macroinvertebrate fauna, mangrove forests, migratory wading birds, nesting turtles and already endangered and vulnerable species of whales and dolphins.