The distribution of invasive and native species in wetlands is determined by hydrological conditions; whereas conditions such as water depth fluctuations, variations in the nutrient concentrations are expected to affect the growth and physiological traits of plants. For the assessment of such effects, we conduct greenhouse experiment with three factors; 1) water depth of 5 cm and 15 cm (static and fluctuated); 2) three levels of nutrient concentrations (i) full‐strength Hoagland solution (N1), (ii) ¼‐strength Hoagland solution (N2), and (iii) ¹/₈‐strength Hoagland solution (N3); and 3) species, invasive Wedelia trilobata (L.) and its congener, native Wedelia chinensis (Osbeck.) under mono and mixed culture. Water depth of 5 cm combined with any of the nutrient treatments significantly restrained the photosynthesis, intracellular CO₂ concentration and leaf chlorophyll of both W. trilobata and W. chinensis. Increase in the water depth to 15 cm with low‐nutrient treatment N3 did not sustain the physiological traits of W. chinensis under mono and mixed planting. A great loss was noted in the growth of W. chinensis at 15 cm static and fluctuated water depth with low‐nutrient treatment (N3) and under mixed culture. In addition, water depth fluctuations with both low‐ and high‐nutrient treatments significantly affected the root‐shoot ratio, relative growth rate, and interspecific interaction among these two species. W. trilobata benefited more from competitive interaction index (CII) under fluctuated water depth at 15 cm with high nutrients, and the value of CII was clearly positive. Therefore, higher competitive ability may contribute to the invasiveness of W. trilobata in wetlands.

All data was collect during the experiment at different intervals. Fresh-weight of shoot, dry-weight of shoot, fresh-weight of root, dry-weight of root, total fresh weight of a plant and total dry biomass of a plant were measured by using weighing scale. Physiological parameters such as net photosynthetic rate, stomatal conductance and intercellular CO₂ concentration were measured by using a portable LI-6400XT, Lincoln, USA photosynthesis measurement system. All these data were recorded during full-sunshine at 9:30–11:30 a.m. once a week during treatments. For leaf chlorophyll measurement, Plant chlorophyll meter, Oakoch OK-Y104, made in China, was used to measure the leaf chlorophyll (Chl) contents (SPAD).  The chlorophyll was noted from the same leaves which were used for photosynthetic measurements.

The dataset is based on the original experimental data which were recored two times per week during whole experiment. All the values are presented in the dataset files, there is no missing values.