Colbricon Superiore and Inferiore are two small adjacent high-mountain lakes located in the Paneveggio Natural Park (Italy) that offer the rare opportunity to study two iso-ecologic water environments differing only by area and volume in a ratio of 2:1 and 3:1, respectively. We took advantage of this setting to investigate phytoplankton dynamics, compare variability and productivity differences between the two basins, and assess size-dependent issues. The phytoplankton group of the Dinophyceae was chosen as the indicator organisms of ecological perturbation owing to their high sensitivity to environmental variations, as well as their acknowledged nature of versatile proxy to report global climatic changes. The study was conducted for over 10 years with fortnightly samplings. Results indicated that (a) the Dinophyceae communities in the smaller lake were significantly more resistant to changes exerted by the fluctuation of lakewater transparency and pH; and (b) the smaller lake sustained a consistently higher production with an average Dinophyceae density 1.73 fold higher than that of the larger lake. The coefficients of variation show that the chemical parameters in the smaller lake display higher time-related fluctuation while being spatially homogeneous and that such conditions correlate with a higher stability of the Dinophyceae assemblage. The use of this setting is also proposed as a model to test relationships between ecosystem production and physical stability.