The Hartbeespoort Dam, located 40 km west of Tshwane on the Crocodile River, is an extremely eutrophic water body. Situated in one of the most economically active areas of South Africa, it receives a high nutrient input from wastewater treatment works (WWTW), leaking sewers, as well as urban and agricultural runoff. The Metsi a Me programme, which ran from 2006 to 2016, aimed to mitigate in-lake nutrient stocks using biomanipulation, including the physical removal of Eichhornia crassipes (water hyacinth) and Microcystis aeruginosa (blue-green algae). Using Department of Water and Sanitation water quality and flow data, the annual influxes and outfluxes of total nitrogen (TN) and total phosphorus (TP) to the Hartbeespoort Dam were calculated. Through literature review and comparison with previous studies, the relative importance of nutrient removal from biomass harvesting in relation to retained nutrients was assessed. The average nutrient influx from rivers during hydrological years 2010/11 to 2016/17 was 582 t∙a−1 TP and 4 687 t∙a−1 TN, with trends for both TN and TP being significantly positive over this period. TP influx increased by 77.8 t∙a−1 every year and TN influx increased by 456 t∙a−1, reversing a long-term negative trend. Average annual dam retention + removal (calculated as the difference between river inputs and outputs, i.e., including sedimentation, biomass removal and denitrification losses) was 358 t P and 2 195 t N. A best estimation of nutrient removal from water hyacinth and algal harvesting was 2.1 t∙a−1 P and 11.5 t∙a−1 N, and 3.9 t∙a−1 P and 40 t∙a−1 N, respectively. An estimated 341 t∙a−1 P and 674–1 288 t∙a−1 N was sedimented. Denitrification losses are poorly quantified but are possibly comparable to sedimentation. River outfluxes increased by 28.4 t∙a−1 TP and 110 t∙a−1 TN, smaller rates than the influxes, suggesting increasing retention per annum. Upgrading WWTWs in the catchment and refurbishing leaking and overflowing sewers is the most appropriate long-term solution.