Solar-induced chlorophyll fluorescence (SIF) has been used to estimate leaf-level net CO assimilation by a mechanistic light reaction (MLR-SIF) equation. However, the application of this model would be limited by the challenging measurement and estimation of input parameters (e.g. fraction of open PSII reaction centres, q). We modified the MLR-SIF model by replacing q by the easily obtained parameters (non-photochemical quenching [NPQ]) to facilitate its application. We employed synchronous measurements of gas exchanges, ChlF parameters and SIF for Leymus chinensis, Populus tomentosa Carrières and Ulmus pumila var. sabulosa under the soil–water deficit and rehydration process to test the robustness of the modified MLR-SIF model. Our results demonstrated that for L. chinensis the net photosynthesis rate dynamics under severe soil–water stress and saturated water condition were effectively captured by the modified MLR-SIF model ( R = 0.75–0.92, RMSE = 1.11–3.56) . For P. tomentosa Carrières and U. pumila var. sabulosa, the net photosynthesis rates were predicted by the modified MLR-SIF model with good accuracy ( R = 0.86, RMSE = 9.44; R = 0.88, RMSE = 4.16) across the water deficit and rehydration condition . However, the electron transport rate estimated by the modified MLR-SIF model uncoupled with the photosynthetic capacity ( r = -0.13) and lowered the net photosynthesis rate simulation precision ( R = 0.35, RMSE = 3.41) for L. chinensis under mild drought stress and saturated light intensities. The electron transport rate estimated by the modified MLR-SIF model downregulated the photosynthetic capacity for P. tomentosa Carrières ( r = 0.32) and U. pumila var. sabulosa ( r = 0.22) under mild drought stress. The shift of the Rubisco and RUBP limited state cross-points, the dynamic photosynthesis parameters across the plant species and the alternative electron sinks under soil–water deficit and rehydration process influenced the simulation precision of the modified MLR-SIF model. Our modified MLR-SIF model provided a basis for understanding and inferring the photosynthetic rate by SIF and NPQ under water stress.