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This series of four papers studies the complex dynamics of water-controlled ecosystems from the hydro-ecological point of view [e.g., I. Rodriguez-Iturbe, Water Resour. Res. 36 (1) (2000) 3–9]. After this general outline, the role of climate, soil, and vegetation is modeled in Part II [F. Laio, A. Porporato, L. Ridolfi, I. Rodriguez-Iturbe, Adv. Water Res. 24 (7) (2001) 707–723] to investigate the probabilistic structure of soil moisture dynamics and the water balance. Particular attention is given to the impact of timing and amount of rainfall, plant physiology, and soil properties. From the statistical characterization of the crossing properties of arbitrary levels of soil moisture, Part III develops an expression for vegetation water stress [A. Porporato, F. Laio, L. Ridolfi, I. Rodriguez-Iturbe, Adv. Water Res. 24 (7) (2001) 725–744]. This measure of stress is then employed to quantify the response of plants to soil moisture deficit as well as to infer plant suitability to given environmental conditions and understand some of the reasons for possible coexistence of different species. Detailed applications of these concepts are developed in Part IV [F. Laio, A. Porporato, C.P. Fernandez-Illescas, I. Rodriguez-Iturbe, Adv. Water Res. 24 (7) (2001) 745–762], where we investigate the dynamics of three different water-controlled ecosystems.