On July 14, 1991, 72,000 L of the pesticide Metam (active ingredient, methyl isothiocyanate) was accidentally released into the Upper Sacramento River. We hypothesized that the spill affected streamside microbial communities and that the effects were persistent. To address this hypothesis, we sampled river soils a year later from sites above and below the spill as well as from an agricultural area and determined soil carbon dioxide efflux (as a measure of soil respiration) in response to methyl isothiocyanate in controlled‐environment microcosms, resulting in estimates of the EC50 and soil degradation rates of methyl isothiocyanate. The soil respiration EC50s for the river soils ranged from 13.2 to 51.4 μg/g methyl isothiocyanate, whereas that of the agricultural soil was 72.2 μg/g. Thus, the soils from the Upper Sacramento River were more sensitive to the toxicologic effects of methyl isothiocyanate than was the agricultural soil. Soils from below the spill site also showed higher (factor two or more) EC50s than soils from reference locations above the spill site. The half‐life of methyl isothiocyanate in soils ranged from 2.7 to 6.9 days and was longer by a factor of two in the river soils. These degradation rates are controlled by both biotic (microbial) and abiotic processes. The presence of a microbial community accelerated the degradation rate by a factor of two. The pattern of EC50 data demonstrates that changes in the microbial community in the river soils were persistent a full year after the spill and that the stress elicited responses that were indicative of physiologic accommodation or selection for resistance at the population, species, and/or community level.