Water is the key element that modulates the provision of goods and services together with global/climate stressors affecting semiarid forests. In this sense, there is a need to improve the understanding and quantification of forest and water relationships as affected by forest management. This work addresses this issue by comparing net rainfall (Pn) redistribution into different belowground hydrological processes (BHP) in two forest types after a thinning treatment: a holm oak coppice (HU) and a post-fire Aleppo pine regeneration (CAL). The relative contribution (RI) of forest structure, antecedent soil moisture (θst), rainfall and meteorological conditions on the BHP was assessed through boosted regression trees models. In both sites, the RI of the forest structure itself was limited (< 10%). However, θst, which clearly increased significantly with thinning, received an average RI of 29%. Surface and subsurface lateral flows showed values < 1% of gross rainfall (Pg) in either site and were not significantly affected by thinning. On the other hand, soil moisture and drainage were affected by the thinning treatment, although with different extent depending on the site: in the drier site (CAL), the increased Pn in the thinning was mainly allocated into increased soil water content, with very limited improvement in drainage (< 10 mm/year); in contrast, in the wetter continental site of HU, drainage to deeper soil layers was the most remarkable effect of thinning (50 mm/year higher than in control), given the higher θst and hence the lower soil water storage available. Thinning also improved the response of BHP during drought, making these processes more elastic and less vulnerable to climatic extremes. The results presented here complement those previously reported on rainfall partitioning in these sites and all together provide a comprehensive understanding of the short-term effect (3–4 years) of water-oriented silviculture in Quercus ilex and Pinus halepensis low-biomass semiarid forests. Questions such as the long-term effects of thinning remain open for these ecosystems.