Densities of submerged vegetation and those of associated animals tend to co-vary. This relationship is often attributed to the positive correlation between the density of vegetation and its protective value against predators. However, two counteracting basic elements underlying this paradigm limit its generality. That is, increasing vegetation density should result in decreased predator–prey encounters, whilst at the same time predator–prey encounters should increase as animal densities increase. These two mechanisms should thus counteract each other when the densities of vegetation and associated animals, including both prey and predators, co-vary. Experimental designs that expose fixed densities of prey and predators to varying densities of vegetation assess only the former mechanism and may thus not properly evaluate the protective value of vegetation in such conditions. By contrast, designs that mimic the naturally co-varying organism densities test both mechanisms and thus their counteractive impacts on predator–prey encounters. We compared the outcomes of the two alternative designs and carried out additional experiments to explain the putative discrepancy. Increasing vegetation density (mimics of Potamogeton pectinatus) enhanced prey (Daphnia magna) survival only when fixed densities of prey and predators (Perca fluviatilis or Rutilus rutilus) were used. When the animal densities were allowed to co-vary with vegetation density, vegetation had no impact on prey survival. Instead, prey survival was determined by the aggregate density of prey and predators, shaped by the species-specific traits of the latter. Thus, the impact of the increased animal densities overrode the impact of the increased vegetation density on predator–prey encounters. It may be insufficient to attribute the co-variation of vegetation, prey and predator densities simply to the association between vegetation density and its protective value. Increased food resources and reduced competition within vegetation may promote prey and thereby also predator abundance to a greater extent than previously thought.