This paper combines environmental science, inorganic chemistry, water quality monitoring and other disciplines to analyze and assess the heavy metals in the water bodies and sediments of the Fenghe River Basin (FRB) in Shaanxi Province, and reveal their sources. The Water Quality Index (WQI), Nemero Index (Pn), Geological Accumulation Index (I-geo) and Potential Ecological Risk Index (RI) are used to assess heavy metals in water and sediments. Pearson correlation analysis (CA), hierarchical cluster analysis (HCA), principal component analysis (PCA) and positive matrix factorization (PMF) models are used to study the relationship and source of heavy metals. The results show that most of the residual heavy metals in the water are below the corresponding environmental quality standards for surface water. Most of the heavy metals in the sediment exceed the background value of the soil. The factors or sources of heavy metals in water and sediment are revealed in detail through PMF models. The main sources of pollution in the region are urban construction and transportation, the electronics industry, machinery manufacturing and tourism. In water, the average contribution rates of these four sources to heavy metals were 36.8%, 11.7%, 9.4% and 42.0%, and in sediments were 8.0%, 29.2%, 23.9% and 38.9%. Therefore, these sectors should be given sufficient attention.