Floating solar photovoltaics (FPV) are emerging as a promising renewable energy technology as global solar energy development ramps up. A growing number of studies have addressed the economic and logistic feasibility of placing and operating FPV on aquatic ecosystems. However, comparatively less research has emphasized their ecological effects. In small lakes and ponds where FPV systems are typically being deployed, the shading caused by the arrays has been associated with reduced phytoplankton growth. As zooplankton feed on phytoplankton and serve as a link in the aquatic food web, potential effects are expected to cascade to higher trophic levels, including fish, amphibians, and birds. In this study we report results of an ecosystem-scale experiment in six fishless freshwater ponds, at the Cornell Experimental Ponds Facility in Ithaca, NY, USA, all of which were dominated by macrophytes. Three of the ponds were partially (70%) covered with FPV arrays, while the other three remained FPV-free and served as controls. Zooplankton samples were collected in the middle and in the edges of all ponds. In the FPV ponds, samples were collected from the gaps between the arrays. In the laboratory, zooplankton was identified to major taxonomic groups, Rotifera, Cladocera, Copepoda Calanoida and Copepoda Cyclopoida, and other abundant potentially heterotrophic groups such as testate amoebae and dinoflagellates. Our results (LMER models) reveal a significant dominance of calanoids (β = -0.51, SE = 0.171, p = 0.0408) in the central areas of ponds with FPV, while cyclopoids (β = -0.897, SE = 0.128, p = 0.0022) dominated along the edges, compared to their respective controls. Additionally, ponds with FPV exhibited a significantly higher presence of the mixotrophic dinoflagellate Ceratium hirundinella (102 Ind.L-1) compared to control ponds (22 Ind.L-1). Our results highlight a potential ecological interaction between FPV and zooplankton communities in ponds.