The prevalence of heavy drinking among college students and its associated health related consequences highlights an urgent need for alcohol prevention programs targeting 18 to 24 year olds. Nevertheless, current alcohol prevention programs in the Netherlands pay surprisingly little attention to the drinking patterns of this specific age group. The study described in this protocol will test the effectiveness of a web-based brief alcohol intervention that is aimed at reducing alcohol use among heavy drinking college students aged 18 to 24 years old. The effectiveness of the What Do You Drink web-based brief alcohol intervention will be tested among 908 heavy drinking college students in a two-arm parallel group randomized controlled trial. Participants will be allocated at random to either the experimental (n = 454: web-based brief alcohol intervention) or control condition (n = 454: no intervention). The primary outcome measure will be the percentage of participants who drink within the normative limits of the Dutch National Health Council for low-risk drinking. These limits specify that, for heavy alcohol use, the mean consumption cannot exceed 14 or 21 glasses of standard alcohol units per week for females and males, respectively, while for binge drinking, the consumption cannot exceed five or more glasses of standard alcohol units on one drinking occasion at least once per week within one month and six months after the intervention. Reductions in mean weekly alcohol consumption and frequency of binge drinking are also primary outcome measures. Weekly Ecological Momentary Assessment will measure alcohol-related cognitions, that is, attitudes, self-efficacy, subjective norms and alcohol expectancies, which will be included as the secondary outcome measures. This study protocol describes the two-arm parallel group randomized controlled trial developed to evaluate the effectiveness of a web-based brief alcohol intervention. We expect a reduction of mean weekly alcohol consumption and frequency of binge drinking in the experimental condition compared to the control condition as a direct result of the intervention. If the website is effective, it will be implemented in alcohol prevention initiatives, which will facilitate the implementation of the protocol.