Many studies done so far on the aquatic ecotoxicity of ionic liquids have dealt with phytoplankton organisms. Nonetheless, benthic organisms are just as important if we are to fully understand the prospective fate and effects of ionic liquids in the aquatic environment. An investigation was therefore undertaken into the toxicity of 1-alkyl-3-methylimidazolium ionic liquids towards the diatom Bacillaria paxillifer and the cyanobacteriumGeitlerinema amphibium, species characteristic of the benthic environment. As in the first part of this study (A. Latała, M. Nędzi and P. Stepnowski, Green Chem., 2009, 11, 580–588), five 1-alkyl-3-methylimidazolium chlorides (from ethyl to decyl) were chosen as the test kit compounds for examining the expected alkyl chain length effect, together with 1-butyl-3-methylimidazolium tetrafluoroborate, dicyanamide, trifluoromethanesulfonate and methyl sulfate and α-methyl[poly(oxy-1,2-ethanediyl)]sulfate for investigating the influence of anions on the toxicity of ionic liquids towards the algal species under investigation. A pronounced alkyl chain effect was found with both organisms. The results indicate that P. amphibium is more sensitive than B. paxillifer. It was also found that the use of trifluoromethanesulfonate and dicyanamide as counteranions in the IL structure gave rise to the most pronounced toxic effects in comparison with the other anions tested. It is assumed that the greater toxicities of long alkyl chain ILs will most probably not pose a greater threat to benthic organisms, since these compounds will undergo rapid and very strong adsorption to sedimentary matter. Short-chain compounds, which are known to be reversibly bound to sediments, may still pose a significant risk to benthic ecosystems, however.