The redistribution of water in semi-arid environments is critical for the maintenance and survival of vegetation patches. We used a systems approach to examine the interactive effects of three engineers—Stipa tenacissima, biological soil crusts, and the European rabbit (Oryctolagus cuniculus)—on infiltration processes in a model gypseous semi-arid Mediterranean grassland. We measured the early (sorptivity) and later (steady-state infiltration) stages of infiltration at two supply potentials using disk permeameters, which allowed us to determine the relative effects of different engineers and soil micropores on water flow through large macropores. We detected few effects under tension when flow was restricted to matrix pores, but under ponding, sorptivity and steady-state infiltration adjacent to Stipa tussocks were 2–3 times higher than in intact or rabbit-disturbed biological soil crusts. Structural Equation Modeling (SEM) showed that both Stipa and biological soil crust cover exerted substantial and equal positive effects on infiltration under ponding, whereas indirectly, rabbit disturbance negatively affected infiltration by reducing crust cover. Under tension, when macropores were prevented from conducting water, Stipa had a direct negative effect and biological soil crust cover was relatively unimportant. More complex SEM models demonstrated that (1) Stipa primarily influenced biological soil crusts by reducing their richness, (2) rabbits exerted a small negative effect on crust richness, and (3) lichens were negatively, and mosses positively, correlated with a derived “infiltration” axis. Our results highlight the importance of biological soil crusts as key players in the maintenance of infiltration processes in Stipa grasslands, and demonstrate the modulating role played by rabbits through their surface disturbances.