This study deals with the examination of quality of seawater bathing areas in Greece over a 10-year period and identifies risk factors for high bacteria indicator organism concentrations. Qualitative descriptive analysis was applied and the microbiological test results of 231,205 water samples were associated with pollution markers and other parameters. Measurements of Escherichia coli (99.6%) and enterococci (100%) were found to be in accordance with the mandatory value guidelines set by the new European Directive. An increasing trend for the yearly mean value of faecal streptococci was noted. Using logistic regression analysis, phenolic smell (OR = 2.10, CI = 2.04–2.16), rainfall the day before sampling (OR = 1.67, CI = 1.64–1.74), high seas (OR = 1.42, CI = 1.39–1.46) and rainfall on the day of sampling (OR = 1.27, CI = 1.20–1.33) were positively independently associated with high levels of bacterial indicators (total coliforms, faecal coliforms, faecal streptococci and E. coli). The highest risk, absolute risk value 42.8% (RR = 3.17, CI = 2.97–3.38), was measured when previous day rainfall, phenolic smell and high seas were simultaneously recorded. Such parameters should be further investigated as predetermining factors for the assessment of beach bathing water quality, providing a timely indication of water risk assessment.