Utricularia stygia Thor and U. intermedia Hayne are aquatic carnivorous plants with distinctly dimorphic shoots. Investment in carnivory and the morphometric characteristics of both types of shoots of these plants were determined in dense stands growing in shallow dystrophic waters in the Třeboň basin, Czech Republic, and their possible ecological regulation and interspecific differences considered. Vertical profiles of chemical and physical microhabitat factors were measured in these stands in order to differentiate key microhabitat factors associated with photosynthetic and carnivorous shoots. Total dry biomass of both species in dense stands ranged between 2.4–97.0 g·m–2. The percentage of carnivorous shoots in the total biomass, which was used as a measure of the investment in carnivory, ranged from 40–59% and that of traps from 18–29% in both species. The high percentage of total biomass made up of carnivorous shoots in both species indicates both a high structural investment in carnivory and high maintenance costs. As the mean length of the main carnivorous shoots and trap number per plant in carnivorous shoots in both species differed highly significantly between sites, it is probable that the investment in carnivory is determined by ecological factors with low water level one of the potentially most important. Marked differences were found only in [O2] between the 1–3 cm deep free-water zone with green photosynthetic shoots of both species and the 10 cm deep loose sediment with chlorophyll-free carnivorous shoots with traps (range 1.7–7.2 vs. 0.0–0.8 mg·l–1). The waters can be characterized as mesotrophic. Though anoxia occurred consistently at a depth of 10 cm in loose sediment at all U. stygia and U. intermedia sites the carnivorous shoots of both species growing in this microhabitat are able to survive and do not avoid this microhabitat.