Leaf area index (LAI, one-sided leaf area per unit ground area) is an important parameter in models of canopy-atmosphere carbon exchange and greenhouse gas fluxes that has been disproportionately under-studied in wetland ecosystems. This study assessed variation in LAI and its sensitivity to canopy height, structure and remotely sensed normalized difference vegetation index (NDVI) in the California Delta, USA in July–August 2014. Plant area index (PAI), an optically measured LAI proxy, significantly varied among wetland sites and vegetation types (p < 0.001). PAI significantly correlated with leaf inclination angle and above-water heights of canopy and standing litter, being on average higher in taller freshwater reeds with steeper leaf angles. Presence of litter contributed to within-site heterogeneity and overestimation of PAI at direct green LAI < 3. Although satellite-based NDVI strongly correlated with PAI (R2 = 0.63, p < 0.001), its application was constrained by presence of water and other non-vegetated backgrounds in wetland pixels. Overall, high within-site variation in LAI resulting from structural heterogeneity and/or vegetation diversity limits representativeness of mean LAI for ecosystem models. This constraint calls for more in-depth future analyses of the effects of vertical and horizontal wetland complexity on LAI measurements and performance as an indicator of light interception and canopy-based ecosystem function.