Copper and zinc are essential micronutrients that are potentially toxic when present in excess in soils. Their bioavailability depends on their speciation in soil, but this may vary with environmental conditions. Aeration and hence redox conditions, and organic matter amendments are among the factors likely to cause variation on metal fractionation. We have monitored the chemical fractionation of both native and added copper and zinc in a clay loam top soil during a 5-month laboratory incubation. The effects of aeration (moist soil or flooded) and addition of two organic matter amendments, alfalfa straw or leaf compost, were studied. Metal spike was more labile than legacy metal, and was slowly redistributed over the incubation period. Organic matter caused short-lived flushes of metals, attributed to metal chelation with soluble organic matter. This effect was greater for straw than for more stable compost. There was no evidence that added organic matter increased the capacity of soil organic matter to immobilise metal. Flooding solubilized soil metal (hydr)oxides, releasing legacy Cu and Zn, but with less effect on the capacity to immobilise metal spike. Effects of flooding and organic matter addition were not additive. Both metals appear to be precipitated as sulphides under reducing conditions, and accounted for in the acid soluble phase. Monitoring the dynamics of metal distribution gives a more comprehensive understanding of underlying processes than would a single measurement, and is closer to in campo conditions than slurry microcosms.