Human-originated transformation in the catchment area may be reflected in the water quality and ecological state of the aquatic environment. Chlorophytes, the most common and diverse group of microalgae, may be a valuable tool for studies of small water bodies, ecosystems poorly recognized but extremely sensitive to the climate changes. Here we investigated the response of the chlorophytes to abiotic and biotic factors in different habitats and ponds’ catchments. Chlorophytes demonstrated a prevalence towards a specific type of catchment area. Field ponds supported chlorophytes typical for nutrient-rich/high-organic and shallow well-mixed waters. Forest ponds supported high chlorophyte diversity. A high importance of desmids, tolerant to light deficiency, confirms their preferences towards lower pH and lower trophic state in the forest ponds. Habitat type strongly impacted the distribution of chlorophytes. Great abundance and fertile-water species were associated with the open water, whereas aquatic plants hosted relatively low chlorophyte abundance which is a derivate of the filtrators grazing as well as the nutrient uptake and shadowing by macrophytes. Macrophyte-dominated zones created favorable conditions for some periphytic desmids and filamentous chlorophytes, species preferring lower trophic state and co-occurring with zooplankton. We assume that cosmopolitan chlorophytes can be adapted for determination of the ecological value of small water bodies, including the level of habitat heterogeneity. But chlorophytes clearly react to the level of human impact in the ponds’ catchment, both specific species and functional groups. Thus, we recommend them, particularly desmids, for water quality state assessment in ponds.