Mortality of total enteric bacteria, Escherichia coli, other coliforms and Salmonella spp. was monitored under municipal effluent irrigated agroforestry plantations via periodic field and in vitro studies. The results of the field study showed no significant differences among agroforestry systems in any of the monitored bacterial populations. Microbial populations were higher in summer (January 2003) than in other seasons. The in vitro study, two pot experiments during October 2003 (pre-summer) and July 2004 (winter), revealed significant effects of moisture on Most Probable Number (MPN) of the total bacteria and E. coli. The moisture levels did not affect the Salmonella spp. and other coliform bacteria, suggesting that certain microbes may be found at low irrigation levels and vice-versa. Enteric microbes were recorded until the 27th day after irrigation in October 2003 and for less than 15 days in July 2004. Thus inclusion of more pathogens in environmental guidelines and stringent exercise of the ‘exclusion’ in practice are suggested.