Water deprivation affects photosynthesis, leaf anatomy, and cell wall composition. Although the former effects have been widely studied, little is known regarding those changes in cell wall major (cellulose, hemicelluloses, pectin, and lignin) and minor (cell wall-bound phenolics) compounds in plants acclimated to short- and long-term water deprivation and during recovery. In particular, how these cell wall changes impact anatomy and/or photosynthesis, specifically mesophyll conductance to CO2 diffusion (gm), has been scarcely studied. To induce changes in photosynthesis, cell wall composition and anatomy, Helianthus annuus plants were studied under five conditions: (i) control (i.e. without stress) (CL); (ii) long-term water deficit stress (LT); (iii) long-term water deficit stress with recovery (LT-Rec); (iv) short-term water deficit stress (ST); and (v) short-term water deficit stress with recovery (ST-Rec), resulting in a wide photosynthetic range (from 3.80 ± 1.05 μmol CO2 m-2 s-1 to 24.53 ± 0.42 μmol CO2 m-2 s-1). Short- and long-term water deprivation and recovery induced distinctive responses of the examined traits, evidencing a cell wall dynamic turnover during plants acclimation to each condition. In particular, we demonstrated for the first time how gm correlated negatively with lignin and cell wall-bound phenolics and how the (cellulose+hemicelloses)/pectin ratio was linked to cell wall thickness (Tcw) variations.