Conifer plantation forestry is recognised as a potential source of diffuse pollution to surface waters and represents a risk to their ecological status. In this study, the water chemistry and Chydoridae (Cladocera) communities of 26 small blanket bog lakes were investigated to assess the impact of plantation forestry. The study was conducted over a 12-month period in 2009-2010 by comparing lakes with three distinct catchment land uses: (i) unplanted blanket bog only present in the catchment, (ii) mature conifer plantation forests only present in the catchment and (iii) catchments containing mature conifer plantation forests with recently clearfelled areas. All three catchment land uses were replicated across two geologies: sandstone and granite. Lakes with afforested catchments had very high concentrations of plant nutrients (P and N), total dissolved organic carbon (TDOC) and heavy metals (Al and Fe), the highest concentrations being recorded from the clearfelled lakes. Similarly, the chydorid communities differed between lakes of contrasting catchment land use. The dominance of Alonopsis elongata in the unplanted blanket bog lakes shifted to dominance by the smaller bodied Chydorus sphaericus, along with Alonella nana, Alonella excisa and Alonella exigua, in the plantation forestry-effected lakes, consistent with a shift in lake trophy. Our findings have shown that plantation forestry can have a profound impact on the water quality of small peatland lakes, especially at the clearfell stage. The response of the chydorid communities is consistent with plantation forestry exerting a trophic, rather than an acidic or toxic, effect on lake ecosystems.