The dataset provides information about the monthly water chemistry of two high-elevation lakes: Bowditch Lake (coordinates: 45°52'30.52"N, 7°52'15.51"E, elevation: 2900 m a.s.l., lake area: 2400 m2) and Cimalegna Lake (coordinates: 45°52'23.17"N, 7°52'37.60"E, elevation: 2800 m a.s.l., lake area: 2700 m2). The Bowditch and Cimalegna lakes are located in the uppermost area and in the middle of the Cimalegna plateau, respectively. The bedrock of both lake catchments is mainly characterised by metamorphic rocks with a predominance of rocks with acid composition, and displaying the secondary presence of basic and terrigenous-carbonatic rocks. Soil (often vegetated) is the main land cover type in the Cimalegna Lake catchment, while coarse sediment constitutes the main land cover type in the Bowditch Lake catchment. Lakes are sampled from 3 points on the shore with no vegetation, at ca. 10-cm depth. The analysed water chemical parameters are: N-NH4 and N-NO3 (period 2007-2020); dissolved organic carbon (DOC), total dissolved nitrogen (TDN), and dissolved organic nitrogen (DON) (period 2011-2020); pH and electrical conductivity (EC) (period 2015-2020).