Species richness of macrophytes of artificial and natural water bodies covering rivers, streams, canals and habitats with standing water was studied in two Central European biogeographical regions, Pannonian and Carpathian, represented by two model areas (the Borská nížina Lowland and the Turčianska Kotlina Basin). We found that: (i) the total number of macrophytes was higher in artificial water bodies compared to natural aquatic habitats in both regions and differences were statistically significant (P<0.05); and (ii) species richness of macrophytes is relatively low in both regions; slightly higher mean number was found in the Pannonian region (3.53) compared with the Carpathian region (3.06). Effects of environmental characteristics on species richness studied by generalized linear model (GLM) showed that explained variances of GLM were similar in both regions. The main drivers of the diversity pattern were those connected with the hydrology of water bodies, such as substrate characteristics and turbidity, less frequent were chemical characteristics, such as water conductivity and N-contents, whereas landscape characteristics manifested the smallest impact.