Agricultural systems that receive high or low organic matter (OM) inputs would be expected to differ in soil nitrogen (N) transformation rates and fates of ammonium (NH4+) and nitrate (NO3-). To compare NH4+ availability, competition between nitrifiers and heterotrophic microorganisms for NH4+ and microbial NO3- assimilation in an organic vs. a conventional irrigated cropping system in the California Central Valley, chemical and biological soil assays, N-15 isotope pool dilution and N-15 tracer techniques were used. Potentially mineralizable N (PMN) and hot minus cold KCl-extracted NH4+ as indicators of soil N supplying capacity were measured five times during the tomato growing season. At mid-season, rates of gross ammonification and gross nitrification after rewetting dry soil were measured in microcosms. Microbial immobilization of NO3- and NH4+ was estimated based on the uptake of N-15 and gross consumption rates. Gross ammonification, PMN, and hot minus cold KCl-extracted NH4+ were approximately twice as high in the organically than the conventionally managed soil. Net estimated microbial NO3- assimilation rates were between 32 and 35% of gross nitrification rates in the conventional and between 37 and 46% in the organic system. In both soils, microbes assimilated more NO3- than NH4+. Heterotrophic microbes assimilated less NH4+ than No-3(-) probably because NH4+ concentrations were low and competition by nitrifiers was 'apparently strong. The high OM input organic system released NH4+ in a gradual manner and, compared to the low OM input conventional system, supported a more active microbial biomass with greater N demand that was met mainly by NO3- immobilization. (C) 2003 Elsevier Science Ltd. All rights reserved.