Risk assessment of toxicants often disregards that environmental conditions, like changing nutrient status, may affect ecosystem response to a toxicant even within an ecosystem. We investigated if effects of pyrene on shallow-water sediments depended on nutrient status of the sediment during 58 days of incubation. Natural undisturbed sediment cores were pre-exposed to two concentrations of inorganic nutrients (nitrogen and phosphorous) for 14 days. After terminating nutrient additions, pyrene was applied once to half the Nu(high) and half the Nu(low) cores in a concentration of 2 mg/kg DW, normalized to 1% TOC. Pyrene affected the sediment systems in both Nu(high) and Nu(low), but effects of pyrene differed between nutrient regimes. In the Nu(low) system, effects of pyrene were mainly seen on the sediment community structure, such as meiofauna community structure. On the contrary, effects of pyrene in Nu(high) were mainly seen on community functions, such as changes in inorganic nutrient fluxes. Direct and indirect effects of pyrene were observed in both nutrient regimes, but they operated on different timescales depending on the variable in focus. This study shows the need to include environmental factors such as nutrient status in risk assessment of toxicants.