The 95th percentile of numbers of intestinal enterococci per 100 mL, associated with estimated health risk, is used for determination of the microbial assessment category (MAC) in the National Guidelines for Managing Risks in Recreational Water published by the Australian National Health and Medical Research Council in 2008. A statistical decision support tool was developed to facilitate the analysis of microbial water quality data for the purposes of classifying recreational waterways in south-east Queensland, Australia. This analysis tool, named ‘EnterosisA’, classifies MACs based on an assessment criterion which takes account of both the calculated 95th enterococci percentile values from empirical data and the associated gastrointestinal illness risk. EnterosisA provides similar functionality to the widely used analysis tool ‘Enterotester’, but is distinguished by a completely different procedure for raw data treatment and by its assessment algorithm. Using enterococci data collected from 88 recreational water sites over the period 2010–2013, the MAC assessment results were compared between Enterotester and EnterosisA. The comparison showed that EnterosisA matched Enterotester MAC results in 86.3 % cases, with 11.4 % over-categorized (over-categorization equates to higher levels of estimated health risk) and 2.3 % under-categorized cases. EnterosisA followed a conservative approach to allocate MACs and aimed to minimize the need for user’s intervention in obtaining the assessment results. Without the involvement of hypothesis testing in the assessment procedure and with a one-click-for-answer design, the EnterosisA is much easier to use. Measured in the raw concentration data scale instead of the standardized distribution scale, the trigger levels estimated by EnterosisA are assumed to be more relevant for recreational water management decision making. The EnterosisA is shown to be a valid, alternative analysis tool in the implementation of the recreational water management guidelines through classifying the microbial water quality of water bodies. This research provides valuable empirical evidence for future revisions of the guidelines.