Canarium madagascariense, an endemic multifunctional tree species native to Madagascar, contributes significantly to the structural integrity of local biodiversity and ecological functions of the rainforest while serving as a source of medicinal resources for local rural communities. Additionally, its fruits are consumed by frugivorous lemurs, which play a vital role in seed dispersal and propagation. This species has been classified as threatened with extinction due to unsustainable timber extraction practices coupled with challenges in natural regeneration and climate change. It may be crucial to understand the correlation between this species and hydric stress for informing reforestation programs, management strategies, and opportunities for biodiversity conservation; however, this aspect remains poorly reported in the existing literature. The main aim of this research was to evaluate the morpho-physiological and biochemical responses of C. madagascariense seedlings subjected to hydric stress and to potassium silicate—a compound known to enhance drought resistance. In this study, 120 seedlings underwent different irrigation levels: 100%, 50%, and 25% of field capacity, both with and without potassium silicate application, under greenhouse conditions. As hydric stress intensified, reductions in diameter and height growth were observed ranging from 40% to 80% and from 42% to 72%, respectively, together with a decline in stomatal conductance from above 0.10 to a critical threshold of 0.001 mol m-2 s-1 from one week of stress. At the same time, the application of potassium silicate did not yield any significant effects on these parameters. In terms of phytochemical analysis, glucose levels nearly doubled in response to increasing stress; however, sucrose was undetectable. Notably, the total phenolic compound content exhibited significant differences with the use of potassium silicate. Specifically, the levels of three phenolic compounds—caffeic acid, epicatechin, and quercetin—were found to decrease markedly in stressed plants when compared to controls. These findings highlighted the potential utility of these molecules as indicators of water stress in C. madagascariense.