Various protocols have been developed for trophic assessment of coastal waters but most incorporate single value compliance criteria for water quality parameters which, in reality, exhibit significant spatial variation. Application of these protocols generally requires the averaging of data recorded at discrete locations to obtain single values for comparison with compliance criteria; however, there is no guarantee that the averaged values are truly representative of overall water quality. The present approach to trophic assessment integrates measurement, remote sensing, flushing analysis and water quality modelling with the aim of identifying sub-regions in coastal waterbodies that demonstrate homogeneity. Averaged water quality data for these homogenous sub-regions should be more representative of the water quality in the sub-region as a whole making the assessment process more accurate. The integrated approach incorporates water quality classification criteria developed by the Irish Environmental Protection Agency but it can incorporate any suitable classification criteria. The approach was validated for a sub-region of Cork Harbour, Ireland and the trophic assessments agreed with previous assessments by the Irish Environmental Protection Agency (EPA). The approach has significant applications in the implementation of the EU Water Framework Directive and was adopted by the Irish EPA in convincing the EU to provide the Irish government with structural funds for water quality management within Cork Harbour. (C) 2011 Elsevier Ltd. All rights reserved.