This research was realized in order to determine and analyze selected heavy metals present in sediment samples from Smolnik creek (Slovakia). The creek is permanently contaminated by acid mine drainage (AMD) from the Pech shaft with average annual flow rates of 6.5 L/s and pH ≈ 4, which acidifies and contaminates surface water and sediment with heavy metals. The pH decreases due to the mixture of AMD with surface water and is followed by metal precipitation and sedimentation in the (aquatic) environment. Potential ecological risk indexes were used to study the pollution status of heavy metals, Cu, Zn, As, and Pb, in sediment and assess their potential ecological risk to the environment. The heavy metals under investigation in the sediment reflected a low ecological risk for both sediment samples (S1 = 68.43; S2 = 53.47). The degree of sediment contamination in the Smolnik creek (Slovakia), for Fe, Mn, Al, Cu, Zn, As, and Pb, has been evaluated using an Enrichment factor, Pollution load index, Geo-accumulation index, single-factor index analysis, Neremo index comprehensive evaluation method, and metal pollution index to compare the total content of metals at the different sampling stations. The high PLI values 1.61 (S1) and 1.54 (S2) indicate strong signs of pollution deterioration. The results from Neremo index comprehensive evaluation method indicate that the S1 location is heavily polluted (3.12) and S2 is moderately polluted (2.95). These results confirmed the fact that the quality of sediment improves with the distance from source of contamination.