In the Anthropocene era, an immersion of toxic substances, i.e., trace metals, has been enhanced in the marine environment not only due to urban sprawl and industrial development but predominantly owing to incongruous management and lack of sustainable approaches. The coastal region of Pakistan shares a similar obstacle as most of the developing countries confronted. Therefore, this study was designed to investigate concentrations of eight metals (Cu, Fe, Zn, Ni, Co, Pb, Cr, and Cd) in sediment and Dotillid crab, Ilyoplax frater, at three tidal creeks in Karachi, Pakistan. All metals in sediments and crabs were analyzed by atomic absorption spectrometer. The sediment pollution was evaluated by contamination degree (CD) and potential ecological risk index (RI). After depicting the metal pollution in sediments, metal accumulation, and contamination in benthic crab were investigated through total metal concentrations in crabs, accumulation factor (AF), correlation analysis, and regression analysis. The results exhibited substantial differences in the concentrations of Zn, Ni, Pb, Cr, and Cd among the tidal creek sediments. Contamination factors indicated that the Cd and Pb had the highest sharing in sediment pollution, and the tidal creeks classified as moderately contaminated. All metal accumulations in Dotillid crabs showed notable spatial variations, and accumulation factors (AFs) for most of the metals were > 1.0, signifying the strong bioaccumulation of metals in crabs. Particularly, Cu, Co, and Cd levels were considerably greater (two to three times) in Dotillid crabs compared to creek’s sediments, even though they don’t share any relationship between two matrixes. Hydrographical and sedimentological traits also revealed significant interactions with metal levels in sediments and crabs. A substantial association was also noticed in Fe, Ni, and Pb between sediments and crabs. Interestingly, most of the metal AFs showed a notable inverse correlation with the environmental matrix. Exceptionally, a strong positive correlation found between the Pb concentration in crabs and sediments suggested that I. frater probably acts as an indicator of Pb pollution.