A protocol to enumerate particle-associated microbial indicator bacteria (heterotrophic plate count [HPC], enterococci [ENT] and Clostridium perfringens [CP]) by membrane filtration in a tropical stream is proposed that relies on high-speed homogenization and chemical treatment. Application of this protocol to stream samples suggest that ENT measurements are more biased by the presence of aggregates than HPC or CP. Whole sample treatment typically increased the colony forming units (CFU) count by 9-52%. Analysis of different settled fractions and examination of the number of indicators recoverable from particles retained on a 5 microm filter in relation to the number of particles containing target indicators both indicate that relatively more ENT form aggregates than HPC or CP. Although the bias is smallest for CP, this does not imply that CP is a better indicator as this depends on the unknown extent to which pathogens are themselves found associated with particles.