Water quality degradation is a serious environmental problem in Nepal especially in urbanized basins. Water sampling was carried out along the heavily urbanized Bagmati drainage network within Kathmandu valley during 2010–2011 in order to evaluate the controlling factors of chemical parameters and to estimate the transport of chemicals from different positions of the landscape. The direct inputs of municipal solid wastes associated with high population density appeared as a prime controlling factor for the variation in chemical parameters and their fluxes. Most of the chemical parameters appeared to increase their concentration with distance downstream. The silicon concentration was much higher than the large river systems of the world and world average probably due to high temperature and high population density. The DOC and TDN concentrations appeared much higher than other pristine river systems in the world. The C:N and N:P ratios were found in the range 0.5–2.6 and 0.3–2.0 respectively along the drainage network. Bisiallitization type of weathering appeared dominantly taking place throughout the basin. The 19.8 and 33.6 tons km⁻² yr⁻¹ of dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) were respectively transported from the outlet point. The cationic denudation rates were 106.4 and 19.6 tons km⁻² yr⁻¹ at the outlet of Bagmati within Kathmandu valley and at the headwater area respectively. The apparent weathering rate appeared five times higher than the actual weathering rate in a heavily urbanized Bagmati basin due to high population density.