Globally, over 230 million people are infected with schistosomiasis, an infectious disease caused by parasitic helminths. Humans can get infected when they contact water which contains Schistosoma parasites. Although the disease can be treated with a drug, people get rapidly reinfected in certain high-transmission settings. Drug treatment alone may not be sufficient to eliminate this disease and additional interventions such as health promotion or improvements in water and sanitation need to be scaled up. To provide recommendations to these control programmes we carried out interdisciplinary research in Eastern Uganda to understand the influence of gender on schistosomiasis risk. We found that the water contact behaviour of boys and girls is quite similar, and we did not see differences in reinfection or genetic diversity of the parasite between boys and girls. Differences in water contact between genders is greater in adults, and further research is required for these individuals. In this setting, infection rates are high in school-aged children and there are no differences between genders. These results emphasise improved control efforts for all school-aged children in communities like these. Our interdisciplinary approach provided complementary findings. Such an integrated approach can therefore have more power to meaningfully inform policy on schistosomiasis control.