The frequency of mass drug administration for schistosomiasis is determined by the community prevalence. This study aimed to assess the influence of seasonality on community prevalence measured by urine microscopy. A cross-sectional study was conducted in primary schools in rural KwaZulu-Natal, South Africa. We collected three urine samples from 622 girls aged 10-12 years, of which 33.9 % were Schistosoma haematobium positive. The measured prevalence was higher just after the high-transmission season (hot season) compared to in the end of the low-transmission season (cool season) (adjusted OR 5.20, 95% CI 4.83 -- 8.33). The log-transformed egg counts in positive cases showed continuous decrease throughout the low-transmission season of 7.4 eggs / mL per month. Our findings show that in rural South Africa, the community prevalence measured in school-aged children is not constant throughout the year. This may be due to a gradual reduction in worm burden after the transmission season. In order to make decisions about eligibility for mass-treatment, urines should be collected shortly after the hottest season in our study area.