Due to their toxicity, lack of bioaccumulation and biodegradability, and ease of binding to sediments, heavy metals are considered the main pollutants of rivers. It is, therefore, necessary to control and monitor these pollutants. The present study analyzed the Krzna River, which flows in southeastern Poland and has an outlet to the Bug River. Over much of its length, the Bug River forms Poland’s border with Belarus, while its origin is in Ukraine. The main purpose of the conducted research was a qualitative and quantitative analysis of selected heavy metals, i.e., Ni, Pb, Zn, Cd, and Cu, in bottom sediments and surface waters of the Krzna River. The secondary objectives were to evaluate the level of contamination of the studied matrices and identify the sources of pollution. Eighty samples of water and bottom sediments from the Krzna River were collected for the analysis. Due to the varying distribution of metals under the influence of changes in temperature, precipitation, and humidity, the samples were collected in May and August 2023. The average cadmium content in the sediments studied was the same in both May and August, at 0.6 mg/kg. In contrast, the nickel content of the sediments ranged from 4.6 to 6.1 mg/kg in May and from 4.8 to 6.8 in August. Only nickel and cadmium of the five heavy metals tested were present in amounts exceeding the geochemical background value. Analysis of the results indicates that only a minimal amount of heavy metals remain dissolved in the surface waters, and the remainder contaminates the sediments. The average concentrations of metals in the studied bottom sediments and surface waters were as follows: zinc > lead > nickel > copper > cadmium. The content of metals in the studied sediments was not high, but at the same time, their presence above the geochemical background indicates anthropogenic human activity. Any changes in hydrodynamic conditions and various environmental factors may result in the re-release of heavy metals contained in sediments into surface waters.