In three microcosm experiments, we exposed microbial communities of a natural sediment to environmentally relevant concentrations of the fungicide captan, the herbicide isoproturon, and the insecticides deltamethrin and pirimicarb. Exposure concentrations were estimated negligible concentrations (NCs), maximum permissible concentrations (MPCs), and 100 times MPC (100MPC). Experimental endpoints were microbial community respiration and biomass, bacterial activity, and denitrification. All four pesticides inhibited bacterial activity by 20 to 24% at MPC, which corresponded to concentrations in the range of μg/kg dry-weight sediment. Treatments with deltamethrin and isoproturon showed inhibiting effects on bacterial activity at NC exposures. Surprisingly, for captan, deltamethrin, and isoproturon, this inhibiting effect was not observed at 100MPC treatments. Microbial biomass was negatively effected in MPC treatments with deltamethrin and in NC treatments with isoproturon. The tested pesticides did not affect community respiration and denitrification rates. These results show that exposure to the tested pesticides may induce toxic responses in sediment microbial communities at concentrations that are predicted to be environmentally safe.