Activity and primary production of two prevailing species Phragmites australis and Carex elata was studied in relation to water level fluctuations on Cerknica Lake. The aim of our research was to examine the role of Phragmites australis and Carex elata in through flow of energy and water cycling in relation to intermittent water regime. On the basis of this research we also wanted to point out the role of both species for the selected ecosystem services and nature conservation aspects. The activity of studied species was monitored measuring photochemical efficiency of PSII, photosynthesis and transpiration rate. On the basis of the latter two we calculated water use efficiency. At the end of the season we performed growth analysis. In Phragmites australis we measured height and density of plants, number of internodes, basal diameter and the number of flowering plants, whilein Carex elata we measured the length and number of leaves. In both we determined leaf area index and dry mass of aboveground plant parts. During field measurements we monitored abiotic parameters such as photosintetically active radiation, relative humidity and air temperature. The study revealed that Phragmites australis and Carex elata played an important role in water cycling and input of energy into the ecosystem. The changes in duration and extent of flooding affected the Phragmites australis to higher extend than Carex elata. Terrestrial reed, as well as reed in water exhibited higher lightuse efficiency during low water level as revealed by negative correlation between photochemical efficiency of PSII and water level. In sedge no difference comparing three seasons were found. Values of potential photochemical efficiency of PSII were not significantly different (near 0.8), that revealed that plants were not under irreversible stress. The level of photosynthesis express growth conditions at the certain time. In littoral reedand in sedge we calculated positive correlation among photosynthesis and water level, while in terrestrial reed the correlation was not significant. The differences in transpiration in terrestrial and littoral reed occurred among different seasons. Positive correlation between transpiration rate and water level was established in both terrestrial and aquatic reeds, while it was not significant in sedge. The results showed that water use efficiency increased under lower water availability. Dry mass of terrestrial reed was in average 1194 g/m2 (year 2005) and somewhat less in 2006 (748 g/m2). Lower production was measured in littoral reed (720 g/m2 and 838 g/m2, respectively). The values in sedge were in average 333 g/m2 and 383 g/m2. The habitus of plants differed among years and locations. In years 2005 and 2006 littoral reed was higher than terrestrial reed. Primary productivity parameters in sedge did not vary among seasons. Three years studies revealed great plasticity of both species to water level fluctuations, that assure undisturbed ecosystem services (input of energy and water cycling), including habitats for other species. Therefore regular water regime is of primary importance for maintenance of favorable growth conditions and consequently the through flow of energy, biodiversity and undisturbed ecosystem services.