Sediment samples from the Gomti River basin were investigated to determine and evaluate trace metal concentrations, their biological effect, and potential ecological and human health risks for adults and children. The mean concentrations of trace metals were organized in the descending order of mercury (Hg) (0.08 mg/kg) > chromium (Cr) (0.06 mg/kg) > lead (Pb) (0.05 mg/kg) > arsenic (As) (0.02 mg/kg) > cadmium (Cd) (0.01 mg/kg). The current study illustrated that metals were attributed to the area from natural sources and different anthropogenic sources especially from industries. However, the concentration levels were lower than the sediment quality guidelines (SQGs) based on the effect-range classifications of threshold effect concentration (TEC) and probable effect concentration (PEC). Therefore, the concentration of the elements showed no adverse biological effects on aquatic organisms. The evaluated potential ecological risk index also revealed the low toxicity to the aquatic environment. Moreover, the applied sediment quality indices, geo-accumulation index (Igeo), contamination factor (CF), and contamination severity index (CSI) suggested that the contamination levels of the elements were in the acceptable range, and the contamination had not notably impacted on the sediment quality. The risk index (HI) concerning age groups was significantly less than the threshold limit of 1 indicating that the contamination had no non-carcinogenic risk effect. The total carcinogenic risk (TCR) was less than a risk value of 1 × 10−4. Hence, the current study suggests that immediate remediation is not required due to an absence of alarming conditions in the study area. Proper monitoring of the attribution of the metal elements should be done for the betterment of human and environmental health.