Despite the importance of water purification to society, it is one of the more difficult wetland ecosystem services to quantify. It remains an issue in ecosystem service assessments where rapid estimates are needed, and poor-quality indicators are overused. We attempted to quantify the water purification service of South African palmiet wetlands (valley-bottom peatlands highly threatened by agriculture). First, we used an instantaneous catchment-scale mass balance sampling approach, which compared the fate of various water quality parameters over degraded and pristine sections of palmiet wetlands. We found that pristine palmiet wetlands acted as a sink for water, major cations, anions, dissolved silicon and nutrients, though there was relatively high variation in these trends. There are important limitations to this catchment-scale approach, including the fact that at this large scale there are multiple mechanisms (internal wetland processes as well as external inputs) at work that are impossible to untangle with limited data. Therefore, secondly, we performed a small field-scale field survey of a wetland fragment to corroborate the catchment-scale results. There was a reasonable level of agreement between the results of the two techniques. We conclude that it appears possible to estimate the water purification function of these valley-bottom wetlands using this catchment-scale approach.