Macroinvertebrate (MI) and macrophyte (MF) communities and their relations were studied in 16 karst ponds on the outskirts of Julian and Kamnik–Savinja Alps. Correlations and influences of environmental factors on the structure of MI and MF communities were investigated. PLOCH procedure was used for sampling of MI, which was conducted with hand net. Later, inventory of MF was performed and their cover values were estimated. MF were determinated and classified into 4 groups according to Ellenberg’s indicator values for humidity of the site. Correlations between environmental factors and parameters of taxonomic richness and diversity of the communities were calculated. Influences of environmental parameters on the structure of communities were analyzed with Canonical Corespondence Analysis and Redundancy Analysis. 10 higher taxa and 23 MI families and 37 aquatic macrophyte species were recorded in surveyed ponds. In ponds with high MF cover and species richness, high MI richness and diversity was also detected. MI richness and diversity were positively correlated with MF richness and diversity, as well as with altitude and pond size. Higher MF cover and MI diversity was in ponds with less intense land use. TP, TNb and stone substrate determined the community structure of MF while land use and oxygen saturation determined the community structure of MI. In ponds MEN2, 3 and JEL2, where the values of both factors was the highest, the highest MI richness and diversity was detected.