Many freshwater ecosystems face severe threats from anthropogenic disturbances. In the field, we investigated the morphology of spring niches and the species richness of vascular plants and bryophytes in 16 springs, draining the quaternary aquifers, located in two different environments—an urban area (city of Białystok) and a protected area (Knyszyn Forest Landscape Park, NE Poland). In total, 47 vascular plant and 45 bryophyte species were recorded, representing mostly crenophytes including protected species. The most important water quality parameters that can be used to evaluate variations of the spring water chemistry in NE Poland are the mineral-related parameters (electrolytic conductivity, Ca2+, SO42−, and Cl−). The organic-related parameters (DOC) and nutrients (TP, NO3−-N) were negatively involved in water quality variations. Our results show that anthropogenic activity significantly affects the biodiversity of plant communities in lowland springs. The presence or absence of crenophytes and bryophytes is indicative of the ecological status of the groundwater outflow complexes.