Little is known about how water deficit affects cotton ( Gossypium hirsutum L.) canopy architecture and the vertical distribution of photosynthesis within the canopy. The objective of this 2-yr field experiment was to determine the effects of reduced water supply on (i) surface area distribution within a cotton canopy, (ii) the transmission of photosynthetically active radiation (PAR) within the canopy, and (iii) the contribution of leaves and non-leaf organs at different positions within the canopy to whole-canopy photosynthesis. The results showed that compared with conventional irrigation, water deficit reduced leaf surface area in the upper canopy layer by 20 to 46% and increased PAR transmission into the mid-canopy layer by 38 to 73%. Slight water deficit reduced leaf photosynthetic rates in the upper canopy layer by 24%, but increased leaf photosynthetic rates in the mid-canopy layer by 23% and the lower canopy layer by 79%. Compared with conventional irrigation, slight water deficit had no significant effect on yield, whereas moderate water deficit significantly reduced both variables. Leaves, especially those in the upper canopy layer, were the main drivers of whole-canopy photosynthesis. On a percentage basis, non-leaf organs accounted for <26% of whole-canopy photosynthesis. Future research is needed to learn more about the photosynthetic potential of non-leaf organs and their response to water deficit.