Colbricon Superiore and Inferiore are two small adjacent high-mountain lakes located in the Paneveggio Natural Park (Italy). The lakes differ by size and depth while sharing the same bedrock setting and catchment basin. Changes in the phytoplankton communities were studied over a 10-years period to individuate which environmental variables would determine the main differences in biotic assemblages across time and between the two lakes.The study was conducted with fortnightly samplings, assessing the density and biomass of algal taxa. Relationships of each of the biological variables with water temperature, pH, conductivity, transparency, water level, previous week rainfall, and relative water column stability were analyzed by correlation and regression analyses, cluster analysis, and by canonical correspondence analysis. The most significant variables resulted air temperature, hydrologic water level and pH. The smaller Colbricon Inferiore had about double the amount of phytoplankton density and biomass than did the larger Colbricon Superiore. The same lake had higher diversity and lower evenness in structure of the phytoplankton community. Notwithstanding their proximity each lake appears to follow independent species composition dynamics, however parallel patterns were interestingly revealed when data were analyzed by pooling taxa into morpho-functional groups. Morpho-functional groups (MFGs) 1b, 3a, 6b, 7a, 9b were differentially most abundant in warm periods, while 2c, 3b, 11c, 5e, 10a prevailed in cold years. MFGs 1b, 2d, 3a and 3b were more characteristic of Lake Colbricon Superiore, while Colbricon Inferiore preferentially featured MFGs 5a, 5e, 9a, 9b, 10a, 11a and 8a. The role of the meteo-climatic parameters was pointed out in driving the different patterns observed in the two lakes.