Due to an indeterminate growth habit, we hypothesised that different canopy layers of cotton might be variably influenced by soil waterlogging. The field-grown cotton cultivar (Sicot 71BRF) was waterlogged at early (WL early , 77 days after planting [DAP]) and late reproductive phases (WL late , 101 DAP) for 120 h. Data from different canopy layers e.g. bottom eight (MSN 1-8 ), middle five (MSN 9-13 ), and upper five main stem nodes (MSN 14+ ) were collected 1 d (post-WL) and 7 d after termination of waterlogging (postrecovery). Both waterlogging events significantly reduced post-WL dry biomass, leaf N concentration and fruit development on MSN 1-8 . In addition, WL early significantly reduced photosynthesis and increased total soluble sugars (TSS) in the MSN 1-8 and MSN 14+ leaves, although MSN 14+ leaves restored photosynthesis, N levels and TSS at recovery. It suggested that WL plants maintained photosynthesis of the upper leaves possibly by transporting N from the lower canopy leaves. Reduction (22%) in seed cotton yield under WL early was the result of fruit loss from first position fruits of the upper and lower sympodial fruiting branches (FB 1-5 and FB 11+ ). Despite restoring the growth through improved photosynthesis and N supply, no yield recovery on FB 11+ suggested that the plants used these assimilates for growth of the established fruits. No significant yield reduction in response to WL late suggested that the established cotton bolls were less sensitive to abscission across all canopy layers.Keywords: Canopy layers, lint yield, growth phase, leaf development, nitrogen re-mobilisation, photosynthesis. Abbreviation: DAP_days after planting; DW_dry weight; FR_fruit retention; FB 1-5 _lower 5 fruiting nodes; FB 5-10 _middle 5 fruiting nodes; FB 11-15 _top 5 fruiting nodes; GB_green bolls; LAI_leaf area index; MS N1-8 _lower 1-8 main stem nodes; MS N9-13 _middle 9-13 main stem nodes; MS N14-18 _top 14-18 main stem nodes; NWL_non-waterlogged; P n _photosynthesis; post-recovery_7 days after termination of waterlogging; post-WL_ day after termination of waterlogging; pre-WL_pre-waterlogging; SLA_specific leaf area; SLN_specific leaf nitrogen; TSS_total soluble sugars; WL early _waterlogging at early reproductive phase; WL late _waterlogging at late reproductive phase; WL_waterlogged.