The invasion of submerged aquatic plants potentially results in a loss of native biodiversity in these ecosystems. There has been little attention paid to the impact of invasive submerged plants on epiphytic algal communities. We conducted a 30-day outdoor mesocosm experiment on the shore of subtropical Lake Liangzihu, China, to investigate the effects of two submerged plant species, an invasive species (Elodea nuttallii) and a native species (Hydrilla verticillata), on epiphytic algal communities. We also explored the relationship between macrophyte secondary metabolites and epiphytic algae by conducting a laboratory cultivation experiment. We give the raw dataste, including the specie data of abundance, epiphytic algal communities traits, and environmental parameters in the outdoor mesocosm experiment and laboratory cultivation experiment, and also including the data of plant traits.

Water samples were collected from a depth of 50 cm in all 15 ponds on the 10^th, 20^th, and 30^th day of the study period. Water temperature (T), dissolved oxygen (DO), pH, turbidity (Turb), and chlorophyll a concentration (Chl-a) were measured using a handheld multi-parameter water analyzer (HYDROLAB HL7, HACH, USA) during field tests. Moreover, we collected 1 L water samples at 50 cm depth from each pond for chemical analysis and immediately stored them on ice. Total nitrogen (TN) and total phosphorus (TP) were analyzed using a flow injection analyzer (QC8500, LACHAT, USA), and dissolved inorganic carbon (DIC) was measured using a total organic carbon analyzer (TOC-L, SHIMADZU, Japan).

At the time of measurement, 50 leaves of Hydrilla verticillata, Elodea nuttallii, and a plant with bionic properties were carefully selected to ensure uniformity in growth state or size before placing them in a wide-mouth plastic bottle with 100 mL of pure water in the respective pond. Epiphytic algae were removed by a soft bristle brush in water (Foerster and Jr, 1965), and the leaf area (LA) was measured using an area meter (LI-3100C, LI-COR, USA) after selection. The 200 mL water samples were split into duplicates, with one piece fixed to 1 mL Lugol's solution for later analysis and another used to determine the maximum quantum efficiency (Fv/Fm) of Photosystem II and Chl-a concentration. The maximum quantum efficiency of Photosystem II of epiphytic algae was determined by Pulse Amplitude Modulation (PAM) fluorometry using a Microscopy Pulse-Amplitude-Modulated fluorometer (Microscopy-PAM, Walz, Germany) (Kottuparambil and Agusti, 2020). The Chl-a concentration of epiphytic algae was determined using a chlorophyll a fluorometer (HYDROLAB MS5, HACH, USA) and used as a surrogate for epiphytic algae biomass  (Yang et al., 2020). The biomass of epiphytic algae (m) was calculated using the following formula: The fixed sample of epiphytic algae was subjected to centrifugation at 2000 rpm for 10 minutes, and the supernatant was discarded. The volume was then adjusted to 30 mL and mixed thoroughly. The number and species of epiphytic algae were enumerated using a counting plate at 400× magnification under an optical microscope (BX53+DP74, OLYMPUS, Japan). For each sample, 50 microscopic fields of vision were examined and counted based on established protocols (Hu and Wei, 2006; Effiong and Inyang, 2015; Qian et al., 2015). Species richness (S) was quantified as the total number of different species present in the sample, while abundance (N, cells·mm^-2) was calculated as the total number of individual cells using the formula:

Prior to the measurements, the maximum quantum efficiency (Fv/Fm) of Photosystem II in the dark was determined using a Diving-PAM fluorometer (DIVING-PAM II, Walz, Germany) (Xu et al., 2018). At the time of measurement, the number of plants in each pond was counted. Plant length was determined for twenty randomly selected plants, while the dry weight of fifty plants within each quadrat was determined by drying at 60°C for >48 h. To calculate the biomass of each plant in the corresponding pond, the dry weight was multiplied by the number of plants and divided by 50.

Afterwards, 1.0 g of fresh plant sample was accurately weighed from each pond for extraction of organic compounds. Organic compounds were extracted by successive extraction from a 1.0 g sample using methanol and a Soxhlet extractor, following the method described by Fileto-Perez et al. (Fileto-Perez et al., 2015). The methanol extract was fixed to a volume of 10 mL and analyzed by GC-MS (GCMS-QP 2020NX, SHIMADZU, Japan). The GC injector temperature was set to 220 °C, and the oven temperature was maintained at 40 °C for 3 min before being increased from 40 °C to 250 °C at 5 °C·min^-1 and maintained at 250 °C for 2 min. The transfer line temperature was set to 250 °C, and helium was used as the carrier gas at a flow rate of 1 mL·min^-1. The MS source was operated in electron impact (EI) mode at 70 eV, and the MS was scanned from 40 to 500 m·z^-1. The concentrations of five classes of secondary metabolites, namely alkaloids, amines, esters, organic acids, and phenols, were determined by summing the relative peak area (RPA) of each class of compounds.