In many sub-Saharan states, despite governments’ awareness campaigns highlighting potential impacts of aquatic pollution, there is a very limited action to protect the riverine systems. Managing the quality of water and sediments needs knowledge of pollutants, agreed standards, and relevant policy framework supporting monitoring and regulation. This study reports metal concentrations in rivers in industrializing Ethiopia. The study also highlights policy and capacity gaps in monitoring of river and sediments. For two sampling periods in 2013 and 2014, chromium (Cr), copper (Cu), zinc (Zn), and lead (Pb) were monitored in water and sediments of the Leyole and Worka rivers in the Kombolcha city, Ethiopia. The sampling results were compared with international guidelines and evaluated against the Ethiopian water protection policies. Chromium was high in the Leyole river water (median 2660 μg/L) and sediments (maximum 740 mg/kg), Cu concentrations in the river water was highest at the midstream part of the Leyole river (median 63 μg/L), but maximum sediment content of 417 mg/kg was found further upstream. Zinc was the highest in the upstream part of the Leyole river water (median 521 μg/L) and sediments (maximum 36,600 mg/kg). Pb concentrations were low in both rivers. For the sediments, relatively higher Pb concentrations (maximum 3640 mg/kg) were found in the upstream of the Leyole river. Except for Pb, the concentrations of all metals surpassed the guidelines for aquatic life, human, livestock, and irrigation water supplies. The median concentrations of all metals exceeded guidelines for sediment quality for aquatic organisms. In Ethiopia, poor technical and financial capabilities restrict monitoring of rivers and sediments and understanding on the effects of pollutants. The guidelines used to protect water quality is based on the World Health Organization standards for drinking water quality, but this is not designed for monitoring ecological health. Further development of water quality standards and locally relevant monitoring framework are needed. Development of monitoring protocols and institutional capacities are important to overcome the policy gaps and support the government’s ambition in increasing industrialization and agricultural intensification. Failure to do so presents high risks for the public and the river ecosystem.