Growing urbanization and land-use changes increase the vulnerability of small freshwater ecosystems to contamination by potentially toxic metals (PTMs). This study presents an integrated assessment of PTMs in water and surface sediments of the Mirusha Waterfall, Kosovo, combining chemical analysis, pollution indices, ecological risk evaluation, and multivariate statistical analysis. Water and sediment samples were collected from six stations (June–July 2024) and analyzed using ICP-OES. In water, copper concentrations ranged from 0.00284 to 0.00287 mg L⁻¹, manganese from 0.67 to 0.79 mg L⁻¹, zinc from 0.95 to 2.36 mg L⁻¹, iron from 0.33 to 0.35 mg L⁻¹, chromium from 0.068 to 0.078 mg L⁻¹, and lead from 0.027 to 0.031 mg L⁻¹. Manganese concentrations exceeded the USEPA guideline value (0.5 mg L⁻¹) at all sampling sites, while iron and lead exceeded selected international guideline thresholds. Sediment metal concentrations were uniformly low (e.g., Cu: 3.85–3.98 mg kg⁻¹; Zn: 1.59–2.41 mg kg⁻¹; Cr: 0.69–0.96 mg kg⁻¹), remaining well below international sediment quality guidelines. Pollution load index (PLI) values ranged from 0.0119 to 0.0139, indicating absence of sediment contamination. The ecological risk index (RI = 1.22–1.61) classified all sites as low ecological risk. Principal component analysis explained 86.7% of total variance (PC1 = 69.4%, PC2 = 17.3%), indicating that metal distributions are predominantly governed by natural geochemical background and hydro sedimentary processes, with limited evidence of strong point-source anthropogenic inputs. Although sediment quality remains good, exceedance of selected guideline values in water highlights the importance of periodic monitoring to ensure long-term ecological protection of this protected freshwater ecosystem.