Even with a national control programme in place, intestinal schistosomiasis continues to be a major public health problem in school-aged children and other community members in Uganda. This is especially the case in the environments around the Great Lakes, where disease transmission is high, such as Lake Victoria. Moreover, in the most remote areas, some schools might periodically miss large-scale drug administrations owing to inaccessibility. To provide contemporary monitoring and surveillance data, 27 schools along the lakeshore were surveyed with a rapid assessment protocol to determine both prevalence and intensity of Schistosoma mansoni and soil-transmitted helminth infections. In total, 25 (92.6%) of schools were positive for S. mansoni, with an average prevalence across the surveyed children of 42% and average infection intensity of 634 eggs per gram of faeces. Mean prevalence of Trichuris trichiura, Ascaris lumbricoides and hookworm was 12.9%, 9.3% and 2.4%, respectively. Results from questionnaire data revealed a high level of itinerancy among the children, and a total of 38.2% reported to have never received treatment for schistosomiasis, despite 96% living in districts targeted by the national control programme. A birthplace outside of Uganda was a significant predictor for increased risk of schistosomiasis infection (odds ratio (OR) = 9.6), and being resident at a school for less than a year was significantly associated with absence of praziquantel treatment (OR = 0.3). Univariate regression analysis showed a trend of increasing schistosomiasis towards the eastern region of Uganda, while semivariograms of infection prevalence demonstrated a range of spatial autocorrelation of ~78 km. Soil-transmitted helminth infections were more common in the Western region. Our results emphasise how social and demographic variables such as migration may affect epidemiological trends and confound the impact of existing treatment regimes.