In Thailand, national standard assessment of water quality is based on fecal coliform bacteria measurement which is a complement to chemical measurement.  The US EPA rapid bioassessment procedures (Barbour, et al, 1999) were applied to test the site classification, level of subsampling, metric selection, metric calibration and index development in the streams of the Loei catchment (Boonsoong et al, 2007).  The purpose of this paper was to extend the previous work.  Fifty sites along the tributaries of the Mekong River, Thailand were investigated in hot dry season, wet season and cool dry season during November 2005 to November 2006.  Fifteen physicochemical parameters of subsurface water were measured to provide ecological information supplement to biological data.  The analysis of benthic assemblages showed discrimination between impaired sites and unimpaired sites in the hot dry and cool dry seasons but it was not clear in the wet season.  The metric selection and calibration of index are in progress.