Planktivorous undesirable fish may threaten both fishpond ecosystem functioning and common carp ( Cyprinus carpio ) farming. The present study revealed a mechanistic understanding of the adverse ecosystem and production impacts that topmouth gudgeon ( Pseudorasbora parva ), an invasive omnivorous fish species from Asia, could represent for eutrophic fishponds in South Bohemia (Czechia). In an outdoor experiment conducted under natural conditions, six similar ponds of small size (ca. 1 ha) were similarly stocked with the same size-class common carps (1+ year-old age cohort). Three ponds were additionally stocked with heterogenous size-class of topmouth gudgeon, other three were control ponds (stocked solely with common carp). Our sampling covered one vegetation season from March to September 2020. Environmental parameters, fish and zooplankton assemblage were sampled monthly, while zoobenthos bimonthly (in April, June and August). To assess the potential effect of overall fish predation and its change during the season, we calculated a fish stock index combining fish density and biomass at the time, referred as FSI C for stocked fish (common carp) and FSI U for undesirable fish (topmouth gudgeon). Some tenfold increase in FSI U reflected an overall effect of topmouth gudgeon predation. Significantly ( p < 0.05) lower FSI C indeed indicated the adverse effect of topmouth gudgeon on the carp populations compared to the control ponds since August. Our results clearly showed a significant top-down effect of topmouth gudgeon on planktonic crustaceans, especially large Daphnia spp. and other cladoceran species. The complete elimination of cladocerans in the second half of the growing season probably contributed to impaired growth of carp and increased consumption of zoobenthos observed in the undesirable fishponds. Our study suggested indeed that water transparency, often used as a simple indicator of water quality in fishponds, did not correspond well with the ecological status, not even biodiversity, of the fishponds under study. The voracious undesirable fish overexploited zooplankton and significantly out-competed commercially reared common carp, which then switched more to foraging on zoobenthos. Thus, efficient eradicating undesirable fish seems to be a superior tool for overall restoring the eutrophic fishpond ecosystems and improving their ecological status. • Voracious undesirable fish cause a threat to carp production and fishpond ecosystem. • Planktivorous fish out-compete carp, which then switch to foraging on zoobenthos. • Eradicating undesirable fish is a superior tool for restoring eutrophic fishponds.