Background Pollen allergies affect a significant proportion of the population globally. At present, Web-based tools such as pollen diaries and mobile apps allow for easy and fast documentation of allergic symptoms via the internet. Objective This study aimed to characterize the users of the Patient’s Hayfever Diary (PHD), a Web-based platform and mobile app, to apply different symptom score calculations for comparison, and to evaluate the contribution of organs and medications to the total score for the first time. Methods The PHD users were filtered with regard to their location in Austria and Germany, significant positive correlation to the respective pollen type (birch/grass), and at least 15 entries in the respective season. Furthermore, 4 different symptom score calculation methods were applied to the datasets from 2009 until 2018, of which 2 were raw symptom scores and 2 were symptom load index (normalized) calculations. Pearson correlation coefficients were calculated pairwise for these 4 symptom score calculations. Results Users were mostly male and belonged to the age groups of 21 to 40 years or ≥40 years. User numbers have increased in the last 5 years, especially when mobile apps were made available. The Pearson correlation coefficients showed a significant linear relationship above 0.9 among the 4 symptom score datasets and thus indicated no significant difference between the different methods of symptom score calculation. The nose contributed the most to the symptom score and determined about 40% of the score. Conclusions The exact method of calculation of the symptom score is not critical. All computation methods show the same behavior (increase/decrease during the season). Therefore, the symptom load index is a useful computation method in all fields exploring pollen allergy, and Web-based diaries are a globally applicable tool to monitor the effect of pollen on human health via electronically generated symptom data.