The effects of different substratum typologies on Posidonia oceanica growth and morphology were estimated in four Sicilian meadows using Generalized and Linear Mixed Models combined with retrodating and biometric analyses. Substratum exerted a multiple effect, resulting in different biometric features for P. oceanica shoots settled on rock from those growing on sand and matte. On rock, values for growth rate, leaf length and shoot surface were lower than those on other substrata, with 42%, 23% and 32% the highest degree of difference respectively. The present study may have interesting methodological consequences for the comprehensive understanding of the causative variables potentially affecting meadows features and their health status. The importance of substratum in the prediction of likely biometry changes in P. oceanica meadows, means that knowledge of substratum type should receive due attention in the future to derive reliable estimates of meadow status. •We examine Posidonia oceanica meadows growing on different substrata.•Variations in P. oceanica morphology and growth depend on substratum type.•On rock the plants show lower growth performance and leaf biometry.•Substratum should be controlled during monitoring the meadows to avoid its confounding.