The Sustainable Agriculture Farming Systems (SAFS) Project was established in 1988 to study the transition from conventional to low-input and organic farm management in California's Sacramento Valley. We evaluated the effects of these alternative farming systems on soil compaction, water-holding capacity, infiltration, and water storage in relation to tomato yield and fruit quality within the SAFS cropping systems comparison 10 years after it had been established. Soil bulk density (0-15, 15-30, 30-45, and 45-60 cm) was not significantly different among the farming systems. In situ water-holding capacity at 24, 48 and 72 h after water application was significantly higher in the organic system at all times and depths except 45-60 cm. Cumulative water infiltration after 3 h in the organic and low-input cover crop-based plots was more than twice that of the conventional system. The more rapid infiltration in the low-input and organic systems resulted in increased total irrigation needs, more water stored in the soil profile throughout the 30 days before harvest, and lower fruit soluble solids and titratable acidity in these systems relative to the conventional system. Yields were not significantly different in the organic, low-input, and conventional systems during either 1997 or 1998.