The importance of nitrogen (N), weeds, and water as yield-limiting factors was evaluated over a 4-year period in tomato cropping systems under conventional, low-input, and organic management. The cropping systems studied were part of the Sustainable Agriculture Farming Systems (SAFS) Project at the University of California, Davis, a comparison of conventional and alternative farming systems in California’s Sacramento Valley. Water applied, soil N levels, plant N uptake, weed abundance, and tomato yield were measured and compared among treatments. Tomato yields ranged from just under 55 to over 90tha⁻¹ and significant treatment differences were observed in 2 of the 4 years. Multivariate analyses, used to sort out the effects of N, weeds, and water, indicated all three factors influenced yields in this study but their relative importance was dependent upon the management system. Results indicated that N availability was most important in limiting yields in the organic system and water availability was more important under conventional management. Although weed abundance was relatively high in the organic system in 2 years of the study, weed competition for N was not evident. Instead, relative N input levels and N immobilization by soil microflora appeared to explain N uptake and tomato yield variation. The findings indicate that organic and low-input tomato systems in this region can produce yields similar to those of conventional systems but that the factors limiting yield may be more difficult to manage.