To clarify the photoprotective mechanisms of cotton leaves under water deficit in the field, leaf gas exchange, chlorophyll a fluorescence as well as the corresponding physiological responses were examined in cotton (Gossypium hirsutum L.) to evaluate electron flux distribution. With increasing water deficit, net photosynthetic rate (Pn) significantly decreased, the total electron flux through PSII [Je(PSII)] gradually decreased and the fraction of electron flux required to sustain CO2 assimilation [Je(PCR)] markedly declined. Simultaneously, the ratio of quantum efficiency of PSII [F(PSII)] to the quantum efficiency of CO2 fixation [F(CO2)] increased, accompanied by an increase in the alternative electron flux (Ja). The enhanced alternative electron flux of O2-dependent Ja(O2-dependent) indicated that electrons had been transported to O2 in the Mehler-peroxide reaction (MPR) and that the remaining alternative electron flux Ja(O2-independent) had been used for nitrate reduction, as indicated by an increase in nitrate reductase (NR) and glutathinone reductase (GR) activities. In addition, mild water deficit increased the proportion of electron flux for the photorespiratory carbon oxidation [Je(PCO)]. Water deficit significantly increased surperoxide radical production rate (O2–•) and hydrogen peroxide content (H2O2), and the activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), peroxidase (POD) and catalase (CAT) in cotton leaves also increased under water deficit. Therefore, the Mehler-peroxidation reaction, photorespiration and nitrate reduction helped to dissipated excess light energy, being important photoprotective mechanisms for adapting the photosynthetic apparatus to mild and moderate water deficit in cotton.