Sheep dipping with organophosphate or synthetic pyrethroid-based formulations is still widely used by farmers in the UK to control ectoparasites and results in 175–220 million litres of spent sheep dip produced each year. Spent sheep dip may be diluted in animal slurry or water prior to disposal onto land. However, the effects of this practice on the microbial ecology of animal slurries, soil and aquatic systems are still relatively unknown. This paper investigated the effect of Bayticol (synthetic pyrethroid sheep dip) and Ectomort (organophosphate sheep dip) concentrations on (i) the survival of 15 protozoan species, (ii) the recovery of the four species of amoebae, and (iii) bacterial survival and growth. This investigation found that overall Bayticol was less toxic to protozoa than Ectomort, with minimum inhibitory concentrations ranging from 0.01 to 0.03% (v/v) and 0.005 to 0.06% (v/v), respectively. Amoebic cysts remained viable and emerged from dormancy, thereby pointing to the potential for recovery of protozoan communities in contaminated environments. The presence of sheep dips did not affect bacterial survival and growth on agar; however, the five test bacteria were not able to utilise the sheep dips as sole carbon sources. These findings have implications for the contamination of animal slurries, soil and aquatic systems, in that there is the potential for significant increases in microbial numbers, containing putative pathogens due to the diminution of bacteriophagous protozoan populations.