Faecal indicator detection in recreational waters is of growing importance in Europe and the rest of the developed world for the safeguarding of the health of users. The EU Bathing Water Directive (BWD) dictates the microbiological water quality standards for European waters using the Faecal indicators: Escherichia coli (E. coli), and Enterococci. Waters are classified as ‘Excellent’, ‘Good’ or ‘Sufficient’. To measure compliance, culture- based tests are widely used and accepted e.g. Colilert 18 from IDEXX or membrane filtration. These methods are reliable and proven but they are slow, typically taking 18 .hours or more to produce a result. These are limited to detecting only Viable-Culturable (VC) cells but not Viable-But-Not-Culturable (VBNC) cells. More rapid results incorporating VBNC detection would allow for more timely and accurate decision- making by governing bodies. This thesis investigates the use of rapid assays based on enzymatic detection to allow for sub 4 hour quantification of E.coli and Enterococci in recreational waters. The work involved improving upon existing enzymatic assays through the introduction of novel reagents and the development of field portable instrumentation for On-site analysis of samples. In this work an enzyme assay for E.coli detection based on β-Glucoronidase activity and the fluorescent substrate 6-Chloro-4-Methylumbelliferone-β-D-glucuronide (6-CMug) was developed. 6-CMug is only recently available (2010) and offered higher fluorescence yield and lower pH sensitivity than previously available substrates such as 4- Methylumbelliferone-β-D-glucuronide (4-Mug). The assay developed offered significant improvements in speed, LOD and sensitivity over existing assays based on 4-Mug. As there is no specific enzyme for the detection of Enterococci culture based assays with specific media were also investigated and a number of detection methodologies were developed. A sensitive field-portable fluorimeter with incubating capability and triplicate sample chambers was designed and built for the on-site analysis of water samples. This development moved beyond state of the art, which was based upon laboratory fluorimeters. The system named ColiSense 1 was designed to conduct a continuous direct enzyme assay for E.coli where the cells were filtered and lysed to release β- Glucuronidase. Data from a one day field trial demonstrated the ability of the system to deliver results on-site within a 75 minute period.