© 2021 Elsevier B.V.Warming, eutrophication, and increased omnivory by small-sized fish are global change processes that induce major effects on the food web structure and primary producers of shallow lakes. Despite the key relevance of phytoplankton and periphyton in freshwaters, the combined and potential synergistic effects of fish omnivory, warming and eutrophication, especially on periphyton, remains little addressed, particularly for subtropical shallow lakes. We experimentally tested the food web effects on phytoplankton and periphyton induced by small visually feeding omnivorous fish (Rhodeus ocellatus), high nutrient enrichment and warming (+4.5 °C) in thirty-two 1000 L-mesocosms simulating littoral conditions of subtropical shallow lakes. We aimed at analysing the mechanisms and responses of periphyton and phytoplankton to these experimental factors. All mesocosms included the submerged macrophytes Vallisneria denseserrulata and Potamogeton lucens and artificial plants at 50% plant volume inhabited, plankton and macroinvertebrates. Small-sized visually feeding omnivorous fish enhanced phytoplankton dominance and periphyton loss. These changes coincided with a decrease in zooplankton biomass and a diversity loss of both zooplankton and macroinvertebrates as well as an increase in snail abundance. Fish presence led to a collapse of cladocerans, thereby releasing the grazing pressure on phytoplankton, and predator and collector macroinvertebrates were replaced with small snails (Radix peregra < 0.5 cm) resulting in enhanced grazing on periphyton. Eutrophication reinforced the fish effects, while warming had weak or no effects. Our results indicate that omnivory by small-sized visually feeding fish may induce stronger effects on the food webs of shallow lakes, towards phytoplankton-dominated states, than the combined effect of nutrient enrichment and warming under the present experimental conditions.