Macrophytes are important elements of aquatic ecosystems that grow in or near water. Their taxonomic composition, species diversity, depth, and density are indicators of environmental health; as such, Macrophytes are used to assess the ecological status of water bodies. Under the aim of assessing the ecological status of the Klina River in Kosovo, a survey was conducted at eight sampling sites along the river course to analyze macrophyte composition, diversity, density, and cover. Three samples were collected at each sampling site from early June to late September. The following macrophyte indices were used to assess the ecological status of the river: Macrophyte Index for Rivers (MIR), River Macrophyte Nutrient Index (RMNI), and River Macrophyte Hydraulic Index (RMHI). Our sampling area included the upper reaches of the river where no organic pollution was detected (oligotrophic), the middle reaches where polluted water from farms is discharged into the river, and the lower reaches characterized by heavy organic pollution from settlements and various industrial activities. There is a positive correlation (p < 0.05) between water temperature, turbidity, electrical conductivity (EC), total dissolved solids (TDS), orthophosphates (PO43−), ammonia (NH4+), nitrites (NO2−), calcium (Ca2+), and potassium (K+) with plant density, RMNI, RMHI, EQR-RMNI, EQR-RMHI, and MIR. Sodium (Na+) has stronger positive correlation (p < 0.01) with RMNI and RMHI indices and negative correlation with EQR-RMNI and EQR-RMHI. Our results show that ecological status along the river varies from high and good upstream to poor, bad, and moderate running downstream.