Organic aquaculture, including carp pond farming, is of growing importance. One of its main characteristics is the health and quality of water environments and maintenance of their biodiversity. In 2013–2014, four organic carp ponds (ORG) in the Waldviertel region (Austria) and four conventional ponds (CONV) in the Třeboň region (Czech Republic), located in the Lainsitz (Lužnice) river basin, were monitored for basic environmental variables, namely hydrochemical and hydrobiological determinants. The aim of this study was to evaluate the performance of organic carp farming technology in the amelioration of carp pond aquatic environment. Aside from temperature, which was probably related to different altitudes, the comparison of physico-chemical environmental variables showed no significant differences between organic and conventional ponds, though dissolved oxygen concentration and saturation, along with turbidity, were higher in ORG ponds, and conductivity was slightly higher in CONV ponds. The mean cumulative richness of zooplankton species was significantly higher in ORG ponds. However, when comparing average richness between both management types, there were significantly fewer rotifer species in ORG fishponds (ORG = 10, CONV = 15; p < 0.01), with total species richness displaying a similar trend (ORG = 17, CONV = 22; p < 0.05). Also zooplankton diversity was significantly (p < 0.05) higher in CONV ponds but no significant difference in zooplankton density and biomass between the two management types was observed in any group of zooplankton. A higher total number of macrozoobenthos taxa was found in CONV ponds (26 taxa) than ORG ponds (10 taxa) and also its cumulative taxa richness was significantly (p < 0.05) higher in CONV ponds (15.8 ± 0.5 taxa) compared with ORG ponds (10.3 ± 0.5 taxa). Despite no significant difference, zoobenthos density was higher in ORG ponds (CONV = 503 ± 113, ORG = 905 ± 682 ind m−2; p > 0.05), while its biomass was higher in CONV ponds (CONV = 5.31 ± 0.48, ORG = 4.45 ± 2.17 g m−2; p > 0.05).