Hyporheic zone (HZ) is an interstitial part of groundwater that can provide a spectrum of subsurface habitats depending on the spatial distribution of upwelling groundwater. Differentiation of environmental factors affects the abundance and distribution of plants associated with outflows of groundwater. Plant communities in spring niches dependence on permanent, relatively cold water that not freeze in winter. High dynamics of redox conditions and low temperature increase the intensity of nitrification, denitrification and ammonification processes. We hypothesized that groundwater upwelling enrich surface water with biogenic compounds, and it depends on among others the flora communities. Research were conducted in two lowland spring niches, its outflows and two rivers in suburbs of Bialystok (Poland). Interstitial samples were collected with mini-piezometers. Nutrient analysis were conducted using chromatographic methods, organic carbon analyser and Kjeldahl analyser. The analysis of flora included: vascular plants and bryophytes. The highest concentration of nutrients was recorded in rivers, which results from the catchment inflow. In interstitial waters of both springs, high concentration of ammonium and nitrate ions was recorded compared to their content in the outflow. Hydrophilic vegetation performs a stabilizing function by assimilating nitrogen compounds and contributing to a variations in nutrients concentration. In total, 19 species of vascular plants, 5 mosses and 1 liverwort were recorded. The springs differed in their richness of species, depending degree of human impact. Brachytecium rivulare, whose presence was recorded, is considered a bioindicator of oligotrophy and mesotrophy. The presence of protected species Nasturtium officinale indicates a high degree of naturalness of the environment. Plant community richness can be a good indicator of the ecological status of lowland springs.