<p>Heavy metal contamination in river systems has become a cause for concern due to complex transport mechanisms. Sediment plays a significant role in the behaviour and fate of metals in aquatic ecosystems. The present study was carried out to investigate seasonal heavy metal contamination (As, Cr, Cu, Fe, and Zn) and the possible response of macrobenthos to wastewater effluent discharge along the longitudinal gradient of the Apies River. The bottom sediment samples were collected from ten (A-J) sites along the longitudinal gradient of the Apies River. Five (<i>n</i> = 5) samples were collected from each site using acid-pretreated bottles. Digestion was carried out using aqua regia, and metal analyses were performed using inductively coupled plasma optical emission spectroscopy (ICP-OES). Macrobenthos were collected through substrate disturbance and the use of a dip net. Sites A and B exhibited negligible to moderate metal concentrations, whereas Sites C—J showed considerable concentrations, with Cr and Cu exceeding the guidelines for aquatic ecosystems. No definite trend was observed for seasonal variation; however, sites immediately after wastewater plant discharge points showed high contamination, which suggests their possible role in metal contamination. Macrobenthos biomass showed a negative correlation with Cr and Cu, and with the contamination degree, pollution load index, and the potential risk index (RI). Heavy metal contamination indices indicated moderate to high contamination from Sites D—J, with the RI signifying low ecological risk. These findings provide an insight into the impact of wastewater effluents on metal enrichment, hence increasing the ecological risk.</p>