Physical separation of natural populations of bacteria from a variety of environments via lectin-mediated magnetic bead separation was undertaken with the aim of obtaining a very clean population of target indigenous bacterial cells suitable for subsequent culture or molecular biological procedures. Recoveries varied with sample type, and were only effective from samples that contained a high culturable population on a general heterotroph agar (R2A) and on MacConkey agar. It was found that use of the lectin concanavalin A enabled selective recovery of coliform bacteria. Escherichia coli was separated with total coliforms, but was not preferentially selected. Separation using indirect magnetic capture was more effective and reliable than direct capture achieved using pre-labelled magnetic beads. The method may ultimately be of use in a monitoring procedure or targeted sampling programme. Copyright (C) 1998 Elsevier Science B.V.