Wetland hydrology is important in understanding wetland systems, evaluating wetland functions and processes and assessing wetland conditions. Wetlands assimilate and transform pollutants and nutrients ensuring that quality water is discharged from the wetland into streams. The objective of this study was to characterise wetland hydrology and evaluate the water quality so as to determine the ecological functioning of the Khalong-la-Lithunya wetland. Wetland hydrology and water quality of the three sub-catchments were monitored from October 2015 to March 2016. Water levels in piezometers were recorded once a month and monthly water levels data for the years 2010, 2011, 2012 and 2013 previously recorded by the Millennium Challenge Account-Lesotho (MCA-L) project were integrated to this study’s data. Rainfall, piezometer and stream water were similarly obtained once every month. These were analysed for δ2H and δ18O water stable isotopes and water quality parameters determined. The estimated overall hydro-period of Khalong-la-Lithunya from the years 2010 to 2016 was 11.4% of the sampled time. The wetland showed delayed response of piezometer water levels to rainfall and additional source of water to the wetland through sub-surface flow. The isotopic composition of piezometer and stream water showed that the water gets stored in the wetland before being discharged to the stream leading to a positive interaction between ground and surface water. Most water quality parameters (Na, pH, Mg, PO4 , COD, BOD, NO3, K, Ca, EC) were higher in streams than in piezometers and were mostly within WHO permissible limits. There was a poorer water quality index in streams (59.71) when compared to that of piezometers (53.67). The principal component analysis (PCA) indicated that the parameters that were responsible for the variation in water quality were related to natural hydro-chemical processes, anthropogenic factors and geology and soil constituents. Temporally most parameters were highest during dry months. Due to a short hydro-period, a delayed interaction between surface and ground water and a poorer stream water quality index, it is concluded that the wetland was not in a good condition. Thus, it is not adequately performing its ecological function.